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parm14sb_all_ash_grouped.rtf
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parm14sb_all_ash_grouped.rtf
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* AMBER 2014SB force-field conversion
* See: http://pubs.acs.org/doi/abs/10.1021/acs.jctc.5b00255
* J. Chem. Theory Comput., DOI: 10.1021/acs.jctc.5b00255
*
23 1
! This is a semi-automated conversion of the AMBER ff14SB force-field, done by
! Dr. Xibing He at Florida State University, in July 2015
! Email: <hexibing_at_gmail.com>
!
! This conversion work is based on the previous work of:
!
! (a) Dr. Thomas E. Cheatham, III, who converted the AMBER Cornell force
! field (ff94):
! http://home.chpc.utah.edu/~cheatham/software.html
! Here is the title section of his conversion file:
! AMBER Cornell et al. (parm94) force field conversion
! See: JACS (1995) 117, 5179-5197.
! nucleic acid part converted by tec3, march 1997
! protein part converted by tec3, february 1999
!
! (b) Dr. Jeff Klauda, who converted the AMBER99 & AMBER99SB in october 2003:
! http://terpconnect.umd.edu/~jbklauda/research/download.html
! Dr. Klauda's conversion work was based on Dr. Cheatham's work.
! For references about AMBER99 & AMBER99SB, see:
! J Comp. Chem. (2000) 21, 1049-1074.
! Proteins, Structure, Function, and Bioinformatics. (2006) 65, 712-725.
!
! What I have done is as following:
! (1) Install AmberTools15, take files described in
! $AMBERHOME/dat/leap/cmd/leaprc.ff14SB:
! parm10.dat, frcmod.ff14SB, amino12.lib, aminoct12.lib, aminont12.lib,
! nucleic12.lib, atomic_ions.lib, and solvents.lib
! (2) Convert parameters in parm10.dat & frcmod.ff14SB to parm14sb_all.prm,
! using Dr. Klauda's parm99SB_all.prm as template.
! (3) Convert the AMBER library files to parm14sb_all.rtf, using Dr. Klauda's
! parm99sb_all.rtf as template.
! (4) Set up tri-neucleic-acid systems (RNA or DNA), such as ADE5-ADE-ADE3
! (RNA), or DOA5-DOA-DOA3 (DNA), for ADE, THY, GUA, CYT, URA.
! load the pdb files into CHARMM and AMBER(Sander) programs, print out the
! bond-, angle-, torsion-, and electrostatic energies, and compare.
! Also, the X-,Y-,Z-forces on each atom are printed out and compared.
! The pdb files fed to CHARMM and AMBER(Sander) have different atom names
! according to their conventions, but with the same atom sequences.
! (5) Set up tri-peptides of all amino acid residues, such as ALA-ALA-ALA,
! ARG-ARG-ARG, ..., patch the N- and C-termini at the ends respectively,
! load the pdb files into CHARMM and AMBER(Sander) programs, print out the
! bond-, angle-, torsion-, and electrostatic energies, and compare.
! Also, the X-,Y-,Z-forces on each atom are printed out and compared.
! The pdb files fed to CHARMM and AMBER(Sander) have different atom names
! according to their conventions, but with the same atom sequences.
! (6) PRES DISU does not exist in Dr. Cheatham's & Dr. Klauda's files.
! it is copied from $CHARMMHOME/toppar/non_charmm/top_amber_cornell.inp
! and modified according to AMBER ff14SB (changing some atom types).
! A small system of two chains is set up, chain A: GLY-CYS-GLY, chain
! B: GLY-CYS-GLY, and S-S bond is formed by patch command. This system
! is tested using CHARMM and AMBER(Sander) respectively, and the resulted
! energies and forces are printed out and compared.
! (7) The topologies of TIP3 water, SOD (Na+), POT (K+) and CLA (Cl-), and the
! parameters are copied from Dr. Cheatham's & Dr. Klauda's files. By the way,
! the VDW parameter of Na+, K+ and Cl- cannot be found in parm10.dat or
! frcmod.ff14SB under the AMBER directory $AmberTools15/dat/leap/parm/, but
! still can be found in parm99.dat, and the parameters agree with those in
! Dr. Cheatham's & Dr. Klauda's files.
! (8) Some orders of atoms in the topology file are adjusted in order to get
! same values of energies and forces from CHARMM and AMBER(Sander).
! For example:
! It's said in Dr. Cheatham & Dr. Klauda's conversion files:
! "TRP: the impropers on "CD1 CD2 CG CB" are giving a slight
! energy and force error that I do not understand at present."
! This problem is solved by changing the atom orders in the declaration
! of improper torsion in TRP from "IMPROPER CD1 CD2 CG CB" to
! "IMPROPER CD2 CB CG CD1".
! Another example:
! In HID, HIE, & HIP, "IMPROPER ND1 CD2 CG CB" is changed to
! "IMPROPER CB CD2 CG ND1"
! (9) The BILD tables from top_all36_na.rtf are used to replace the IC tables
! in Dr. Klauda & Dr. Cheatham's conversion files for:
! ADE, URA, THY, CYT, GUA
! These tables matter if you want to generate coordinates automatically
! using CHARMM program instead of reading coordinates from files.
! The old IC tables for nucleic residues are abandoned because they bring
! a "level -1" error for a test case. Thanks to Prof. Alexander MacKerell
! (University of Maryland, Baltimore) for the test case.
!
! Note: The energies and forces agree to within ~0.0002 (mostly within ~0.0001)
! using both CHARMM and AMBER. A longrange cutoff of 80 Angstroms was used
! for both AMBER and CHARMM.
!
! Note: In order to compare energies and forces correctly, CHARMM program should
! "be compiled with the AMBER keyword added to pref.dat, to get an exact match:
! a hard-coded electrostatic constant is different for CHARMM and AMBER force
! fields" (said by Rick Venable, et al. on CHARMM Forum).
! Also see below for details about the constant.
!
! Note: Although I have done some test jobs, there is NO guarantee. Therefore,
! USE AT YOUR OWN RISK!
!
! For protein residues, changes of atom types from AMBER ff99SB to ff14SB:
! CT -> CX, for p3 aliphatic C, alpha-C in protein residues.
! CT -> C8, for sp3 aliphatic C, -CH2-, in side chain of ARG & LYS
! CT -> 2C, for sp3 aliphatic C, -CH2-, in side chain of ASN ASP CYS CYX GLH GLH
! GLN GLU ILE LEU MET SER
! CT -> 3C, for sp3 aliphatic C, -CH-, in side chain of ILE LEU THR VAL
! C -> CO, for sp2 C carboxylate group, in side chain of ASP & GLU
! SH -> S , for S in CYX
!
! As to the nucleic acids, some atom types are also changed from ff99SB to ff14SB:
! CT -> CI, for atom name C5' in ADE URA THY CYT GUA and their patches
! CM -> CS, for atom names C6 & C5 in URA (not in patches)
! CM -> C4, for atom names C6 & C5 in CYT (not in patches)
! CK -> CP, for atom name C8 in GUA (not in patches)
!
! In Dr. Cheatham & Dr. Klauda's conversion files, AMBER atom types with "*"
! in the name, N* and C*, were renamed to NS and CS, respectively. However,
! in AMBER ff14SB, atom type CS already exists. Therefore, here N* and C*
! are renamed to NG and CG, respectively.
!
!
! The following remarks are copied from Dr. Cheatham & Dr. Klauda's conversion
! files:
!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
! WARNING! Please read through all the comments here in order to
! properly understand how to set up a CHARMM run with this force
! field and to properly understand the limitations and potential
! errors...
!
! NOTE: the charges here are un-scaled and represent the
! exact AMBER charges. See the comment on the electrostatics below.
!
! Standard CHARMM residue names are utilized:
!
! ADE, THY, GUA, CYT, URA.
!
! ALA, ARG, ASN, ASP, CYS, CYM, CYX, GLN, GLU, GLH,
! GLY, HID, HIE, HIP, ILE, LEU, LYS, MET, PHE, PRO,
! SER, THR, TRP, TYR, VAL, ACE, NME
!
!
! Atom type names conform to the AMBER Cornell et. al. 1995,
! parm99.dat, all_nuc94.in, and all_amino* naming conventions
! where possible. Exceptions to this rule include types with "*"
! in the name (i.e. N*, C*). CHARMM atom names are utilized
! except for sodium.
! To build the residues, the BILD arrays from the top_all22_na.inp were
! utilized (since these are actually probably more trustworthy then
! those supplied in AMBER) and modified where necessary (i.e. THY).
! They may not be reliable in all cases. BONDS were also copied from
! top_all22_na.inp and all angles and dihedrals autogenerated.
! The impropers were taken straight from the AMBER residue topology
! files (and placed in proper order). All this was done by hand editing.
!
! Results were checked by comparing energies and forces for all the
! residues defined herein. In general, in simulations performing a
! single energy and force evaluation with a cutoff large enough to
! span the entire system the energies and forces agree
! to within ~0.0005 using both CHARMM and AMBER. A longrange cutoff
! of 80 Angs. was used for both AMBER and CHARMM. The AMBER energies
! and forces were calculated using AMBER 7 sander
! (with &debugf to print out atomic forces to forcedump.dat) and CHARMM
! c31a1 (ener and coor force comp and print coor comp). Note that
! differences in the forces may be apparent if the coordinates do not
! match exactly or in cases where different constants are used between
! AMBER and CHARMM. These points require a little more elaboration.
!
! Differences in the coordinates:
!
! (*) incorrect mapping between AMBER and CHARMM coordinates
! (i.e. not 1-to-1). This is possible with hand editting of the
! AMBER names to convert to CHARMM if the correct mapping isn't
! followed. The only case that was readily apparent in this
! analysis was incorrect mapping of H2' and H2'' in the DNA
! residues of ADE, GUA and CYT. The rename command can be used
! to swap names and alleviate this problem (which is not a real
! problem except when comparing forces).
!
! (*) parm coordinate precision. If the parm coordinates were
! created from a PDB file using the link-edit-parm path, improper
! conversion from text->binary->text in edit/parm leads to
! differences in the parm coordinates from the PDB file.
! Therefore, the coordinates will be different than those
! generated by CHARMM using the same PDB coordinates. Therefore,
! prior to comparing forces, the PDB should be converted directly
! to the parm coordinates (which can be done using xleap).
!
! Differences in the electrostatic energies:
!
! (*) The conversion from charge units to kcal/mol in CHARMM is based
! on the value 332.0716 whereas AMBER uses 18.2223**2 or 332.0522173.
! The actual value is somewhat lower than both these values
! (~331.843)! To convert the charges to "CHARMM", they should be
! multiplied by 1.000058372. This was not done within this file.
! [When this is done, the charges are not rounded and therefore
! non-integral charges for the residues are apparent.] To get around
! this problem either the charges can be scaled within CHARMM (which
! will still lead to non-integral charge) or in versions of CHARMM
! beyond c25n3, and through the application of the "AMBER" keyword in
! pref.dat, the AMBER constant can be used. By default, the "fast"
! routines cannot be used with the AMBER-style impropers. In the
! later versions of CHARMM, the AMBER keyword circumvents this
! problem.
!
! BUILDING NUCLEIC ACID STRUCTURES:
!
! To build residues, use the standard naming conventions. By default
! the 5ter and 3ter patchs are applied which convert the first
! residue to a 5'-hydroxyl (no terminal phosphate) and the last
! residue to a 3'-hydroxyl.
!
! NOTE that in the case of case of ADE, GUA and CYT, by default the
! system is RIBONUCLEIC acid. To convert to deoxyribose, use the
! following patchs:
!
! patch DOA5 segid residue <-- 5'-terminal ADE
! patch DOA segid residue <-- standard ADE
! patch DOA3 segid residue <-- 3'-terminal ADE
! patch DOC5 segid residue <-- 5'-terminal CYT
! patch DOC segid residue <-- standard CYT
! patch DOC3 segid residue <-- 3'-terminal CYT
! patch DOG5 segid residue <-- 5'-terminal GUA
! patch DOG segid residue <-- standard GUA
! patch DOG3 segid residue <-- 3'-terminal GUA
!
! ...where "segid" is the current segment and "residue" is the
! residue number
!
! As an example, let's build a single stranded DNA, d[CATG]. We need
! to apply 5' and 3' terminal patches and also patches to turn the
! RNA into DNA for each residue (except THY which is DNA).
!
! read sequence card
! 4
! CYT ADE THY GUA
! generate s1 setup
! patch doc5 s1 1
! patch doa s1 2
! patch dog3 s1 4
!
!
! PROTEIN PARAMETERS:
!
! note: isolated amino acids have not been tested, only tri-peptides
! with the same amino acids in the chain, i.e. ala-ala-ala, etc.
! have been tested with charged terminii (i.e. nala-ala-cala).
! The patches to the terminii (for each residue append N for the
! N-terminal or C for the C terminal) are applied automatically
! to the first/last residues. In general the energy/force comparison
! is as good as with the nucleic acid parameters, but do note that as
! the energy increases (such as with large van der Waals overlap) the
! absolute agreement no longer is as good. This may relate to (1)
! slight coordinate differences between AMBER/CHARMM and (2)
! numerical differences due to differing operations in the
! calculation. In any event, equivalent parameters are used and
! there is an equivalent number of bonds/angles/dihedrals, etc.
! between the CHARMM PSF files and AMBER prmtop files.
!
! PROTEIN CONVERSION NOTES:
!
! (1) there are no terminal CYM (negatively charged CYS) residues
! within the Cornell et al. force field. The CYM and CYX
! residues were not tested for reliability. Use at own risk.
! (2) GLH, or neutral glutamic acid isn't available as a C- or N-
! terminal residue. This has not been tested for reliability;
! use at own risk. Note also that the IC table was not modified
! to include the extra hydrogen...
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!
! AMBER atom types and masses (from parm10.dat & frcmod.ff14SB)
!
MASS -1 C 12.01000 ! sp2 C carbonyl group
MASS -1 CA 12.01000 ! sp2 C pure aromatic (benzene)
MASS -1 CB 12.01000 ! sp2 aromatic C, 5&6 membered ring junction
MASS -1 CC 12.01000 ! sp2 aromatic C, 5 memb. ring HIS
MASS -1 CD 12.01000 ! sp2 C atom in the middle of: C=CD-CD=C
MASS -1 CI 12.01000 ! parmbsc0
MASS -1 CK 12.01000 ! sp2 C 5 memb.ring in purines (dA,dG)
MASS -1 CP 12.01000 ! sp2 C 5 memb.ring in purines (G)
MASS -1 CM 12.01000 ! sp2 C pyrimidines in pos. 5 & 6 (dT,dC)
MASS -1 CS 12.01000 ! sp2 C pyrimidines in pos. 5 & 6 (U)
MASS -1 CN 12.01000 ! sp2 C aromatic 5&6 memb.ring junct.(TRP)
MASS -1 CQ 12.01000 ! sp2 C in 5 mem.ring of purines between 2 N
MASS -1 CR 12.01000 ! sp2 arom as CQ but in HIS
MASS -1 CT 12.01000 ! sp3 aliphatic C
MASS -1 CV 12.01000 ! sp2 arom. 5 memb.ring w/1 N and 1 H (HIS)
MASS -1 CW 12.01000 ! sp2 arom. 5 memb.ring w/1 N-H and 1 H (HIS)
MASS -1 CG 12.01000 ! sp2 arom. 5 memb.ring w/1 subst. (TRP)
MASS -1 CX 12.01000 ! protein C-alpha (new to ff10)
MASS -1 CY 12.01000 ! nitrile C (Howard et al.JCC,16,243,1995)
MASS -1 CZ 12.01000 ! sp C (Howard et al.JCC,16,243,1995)
MASS -1 C5 12.01000 ! sp2 C 5 memb.ring in purines (A)
MASS -1 C4 12.01000 ! sp2 C pyrimidines in pos. 5 & 6 (C)
MASS -1 CO 12.01000 ! sp2 C carboxylate group
MASS -1 2C 12.01000 ! sp3 aliphatic C with two (duo) heavy atoms
MASS -1 3C 12.01000 ! sp3 aliphatic C with three (tres) heavy atoms
MASS -1 C8 12.01000 ! sp3 aliphatic C basic AA side chain
MASS -1 C0 40.08000 ! calcium
MASS -1 H 1.00800 ! H bonded to nitrogen atoms
MASS -1 HC 1.00800 ! H aliph. bond. to C without electrwd.group
MASS -1 H1 1.00800 ! H aliph. bond. to C with 1 electrwd. group
MASS -1 H2 1.00800 ! H aliph. bond. to C with 2 electrwd.groups
MASS -1 H3 1.00800 ! H aliph. bond. to C with 3 eletrwd.groups
MASS -1 HA 1.00800 ! H arom. bond. to C without elctrwd. groups
MASS -1 H4 1.00800 ! H arom. bond. to C with 1 electrwd. group
MASS -1 H5 1.00800 ! H arom.at C with 2 elctrwd. gr,+HCOO group
MASS -1 HO 1.00800 ! hydroxyl group
MASS -1 HS 1.00800 ! hydrogen bonded to sulphur (pol?)
MASS -1 HW 1.00800 ! H in TIP3P water
MASS -1 HP 1.00800 ! H bonded to C next to positively charged gr
MASS -1 HZ 1.00800 ! H bond sp C (Howard et al.JCC,16,243,1995)
MASS -1 F 19.00000 ! fluorine (not fluoride!)
MASS -1 Cl 35.45000 ! chlorine (Applequist) (not chloride!)
MASS -1 Br 79.90000 ! bromine (Applequist) (not bromide!)
MASS -1 I 126.90000 ! iodine (Applequist) (not iodide!)
MASS -1 MG 24.30500 ! magnesium
MASS -1 N 14.01000 ! sp2 nitrogen in amide groups
MASS -1 NA 14.01000 ! sp2 N in 5 memb.ring w/H atom (HIS)
MASS -1 NB 14.01000 ! sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA)
MASS -1 NC 14.01000 ! sp2 N in 6 memb.ring w/LP (ADE,GUA)
MASS -1 N2 14.01000 ! sp2 N in amino groups
MASS -1 N3 14.01000 ! sp3 N for charged amino groups (Lys, etc)
MASS -1 NT 14.01000 ! sp3 N for amino groups amino groups
MASS -1 NG 14.01000 ! sp2 N
MASS -1 NY 14.01000 ! nitrile N (Howard et al.JCC,16,243,1995)
MASS -1 O 16.00000 ! carbonyl group oxygen
MASS -1 O2 16.00000 ! carboxyl and phosphate group oxygen
MASS -1 OW 16.00000 ! oxygen in TIP3P water
MASS -1 OH 16.00000 ! oxygen in hydroxyl group
MASS -1 OS 16.00000 ! ether and ester oxygen
MASS -1 OP 16.00000 ! 2- phosphate oxygen
MASS -1 P 30.97000 ! phosphate,pol:JACS,112,8543,90,K.J.Miller
MASS -1 S 32.06000 ! S in disulfide linkage,pol:JPC,102,2399,98
MASS -1 SH 32.06000 ! S in cystine
!MASS -1 CU 63.55 ! copper
!MASS -1 FE 55.00 ! iron
MASS -1 Zn 65.40000 ! Zn2+
MASS -1 EP 0.00000 ! extra point
MASS -1 SOD 22.99000 ! Na+
MASS -1 POT 39.10000 ! K+
MASS -1 CLA 35.45000 ! Cl-
DECL -CA ! proteins
DECL -C
DECL -O
DECL +N
DECL +H
DECL +CA
DECL +P ! nucleic acids
DECL +O1P
DECL +O2P
DECL +O5'
DECL -O3'
DEFAULT FIRST NTER LAST CTER
AUTOGENERATE ANGLES DIHEDRAL
!
! WATER & IONS
!
RESI TIP3 0.00 ! TIPS3P WATER MODEL
! GENERATE USING NOANGLE NODIHEDRAL
GROUP
ATOM OH2 OW -0.834
ATOM H1 HW 0.417
ATOM H2 HW 0.417
BOND OH2 H1 OH2 H2 H1 H2 ! THE LAST BOND IS NEEDED FOR SHAKE
ANGLE H1 OH2 H2 ! REQUIRED
PATCHING FIRS NONE LAST NONE
RESI SOD 1.00 ! Na+ Aqvist JPC 1990,94,8021. (adapted)
GROUP
ATOM SOD SOD 1.00
PATCHING FIRST NONE LAST NONE
RESI POT 1.00 ! K+ Aqvist JPC 1990,94,8021. (adapted)
GROUP
ATOM POT POT 1.00
PATCHING FIRST NONE LAST NONE
RESI CLA -1.00 ! Cl- Smith, JCP 1994,100:5,3757.
GROUP
ATOM CLA CLA -1.00
PATCHING FIRST NONE LAST NONE
!
! nucleic
!
RESI ADE -1.0 ! note: this is RNA, resname A in ff14SB, RA in ff99SB
ATOM P P 1.1662
ATOM O1P O2 -0.7760 ! note: name is OP1 in ff14SB, O1P in ff99SB
ATOM O2P O2 -0.7760 ! note: name is OP2 in ff14SB, O2P in ff99SB
ATOM O5' OS -0.4989
ATOM C5' CI 0.0558 ! note: type changed from CT (ff99SB) to CI (ff14SB)
ATOM H5' H1 0.0679 ! note: name is H5'1 in ff99SB
ATOM H5'' H1 0.0679 ! note: name is H5'2 in ff99SB
ATOM C4' CT 0.1065
ATOM H4' H1 0.1174
ATOM O4' OS -0.3548
ATOM C1' CT 0.0394
ATOM H1' H2 0.2007
ATOM N9 NG -0.0251 ! note: type is N* in ff14SB & ff99SB
ATOM C8 C5 0.2006
ATOM H8 H5 0.1553
ATOM N7 NB -0.6073
ATOM C5 CB 0.0515
ATOM C4 CB 0.3053
ATOM N6 N2 -0.9019
ATOM H61 H 0.4115
ATOM H62 H 0.4115
ATOM C6 CA 0.7009
ATOM C2 CQ 0.5875
ATOM H2 H5 0.0473
ATOM N1 NC -0.7615
ATOM N3 NC -0.6997
ATOM C3' CT 0.2022
ATOM H3' H1 0.0615
ATOM O3' OS -0.5246
ATOM C2' CT 0.0670
ATOM H2'' H1 0.0972 ! note: name is H2' in ff14SB, H2'1 in ff99SB
ATOM O2' OH -0.6139
ATOM H2' HO 0.4186 ! note: name is HO2' in ff14SB, HO'2 in ff99SB
! using charmm bond lists (top_all22_na.inp)
BOND P O1P P O2P P O5'
BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1'
BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3
BOND C4 C5 N3 C2 C2 N1 N1 C6 C6 N6
BOND N6 H61 N6 H62 C6 C5 C5 N7 N7 C8
BOND C2' C3' C2' O2' O2' H2' C3' O3' O3' +P
BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5'
BOND C5' H5'' C8 H8 C2 H2
IMPROPER C4 C8 N9 C1'
IMPROPER C6 H61 N6 H62
IMPROPER N7 N9 C8 H8
IMPROPER N1 N3 C2 H2
IMPROPER C5 N6 C6 N1
DONO H61 N6
DONO H62 N6
DONO H2' O2'
ACCE N3
ACCE N7
ACCE N1
ACCE O1P P
ACCE O2P P
ACCE O2'
ACCE O3'
ACCE O4'
ACCE O5'
! build array from charmm (top_all36_na.rtf)
IC -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha
IC -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802
IC -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801
IC P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta
IC O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284 !gamma
IC C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212 !delta
IC C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001 !epsilon
IC C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996 !zeta
IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160
IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212
IC C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251 !puck
IC C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896
IC O4' C1' N9 C4 1.5251 113.71 -97.2 125.59 1.3783 !chi
IC C1' C4 *N9 C8 1.4896 125.97 -179.94 106.0 1.367
IC C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312
IC C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382
IC C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0
IC N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0
IC C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0
IC N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342
IC C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337
IC N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01
IC H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01
IC C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337
IC N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01
IC H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01
IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0
IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0
IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212
IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284
IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0
IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0
IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0
IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0
IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0
IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0
PATCH FIRST ADE5 LAST ADE3
RESI URA -1.0 ! note: this is RNA, resname U in ff14SB, RU in ff99SB
GROUP
ATOM P P 1.1662
ATOM O1P O2 -0.7760 ! note: name is OP1 in ff14SB, O1P in ff99SB
ATOM O2P O2 -0.7760 ! note: name is OP2 in ff14SB, O2P in ff99SB
ATOM O5' OS -0.4989
GROUP
ATOM C5' CI 0.0558 ! note: type changed from CT (ff99SB) to CI (ff14SB)
ATOM H5' H1 0.0679 ! note: name is H5'1 in ff99SB
ATOM H5'' H1 0.0679 ! note: name is H5'2 in ff99SB
GROUP
ATOM C4' CT 0.1065
ATOM H4' H1 0.1174
ATOM O4' OS -0.3548
GROUP
ATOM C1' CT 0.0674
ATOM H1' H2 0.1824
ATOM N1 NG 0.0418 ! note: type is N* in ff14SB & ff99SB
GROUP
ATOM C6 CS -0.1126 ! note: type changed from CM (ff99SB) to CS (ff14SB)
ATOM H6 H4 0.2188
GROUP
ATOM C5 CS -0.3635 ! note: type changed from CM (ff99SB) to CS (ff14SB)
ATOM H5 HA 0.1811
GROUP
ATOM C4 C 0.5952
ATOM O4 O -0.5761
GROUP
ATOM N3 NA -0.3549
ATOM H3 H 0.3154
GROUP
ATOM C2 C 0.4687
ATOM O2 O -0.5477
GROUP
ATOM C3' CT 0.2022
ATOM H3' H1 0.0615
ATOM O3' OS -0.5246
GROUP
ATOM C2' CT 0.0670
ATOM H2'' H1 0.0972 ! note: name is H2' in ff14SB, H2'1 in ff99SB
GROUP
ATOM O2' OH -0.6139
ATOM H2' HO 0.4186 ! note: name is HO2' in ff14SB, HO'2 in ff99SB
! bonds from charmm (top_all22_na.inp)
BOND P O1P P O2P P O5'
BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1'
BOND C1' N1 C1' C2' N1 C2 N1 C6 C2 O2
BOND C2 N3 N3 H3 N3 C4 C4 O4 C4 C5
BOND C5 C6 C2' C3' C3' O3' O3' +P
BOND C2' O2' O2' H2'
BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5'
BOND C5' H5'' C5 H5 C6 H6
IMPROPER C2 C6 N1 C1'
IMPROPER C4 C6 C5 H5
IMPROPER N1 N3 C2 O2
IMPROPER C5 N3 C4 O4
IMPROPER C2 C4 N3 H3
IMPROPER N1 C5 C6 H6
DONO H3 N3
DONO H2' O2'
ACCE O2 C2
ACCE O4 C4
ACCE O1P P
ACCE O2P P
ACCE O2'
ACCE O3'
ACCE O4'
ACCE O5'
! build array from charmm (top_all36_na.rtf)
IC -O3' P O5' C5' 1.6001 101.45 -39.25 119.00 1.4401
IC -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802
IC -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801
IC P O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160
IC O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284
IC C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212
IC C4' C3' O3' +P 1.5284 111.92 159.13 119.05 1.6001
IC C3' O3' +P +O5' 1.4212 119.05 -98.86 101.45 1.5996
IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160
IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212
IC C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251
IC C3' C2' C1' N1 1.5284 101.97 144.39 113.71 1.4896
IC O4' C1' N1 C2 1.5251 113.71 -96.0 117.06 1.3746
IC C1' C2 *N1 C6 1.4896 117.06 -180.0 121.3 1.379
IC C2 N1 C6 C5 1.379 121.3 0.0 122.8 1.338
IC C6 N1 C2 N3 1.380 121.3 0.0 114.8 1.373
IC N1 N3 *C2 O2 1.379 114.8 -180.0 122.0 1.218
IC N1 C2 N3 C4 1.379 114.8 0.0 127.0 1.383
IC C5 N3 *C4 O4 1.440 114.7 180.0 119.8 1.227
IC C2 C4 *N3 H3 1.373 127.0 180.0 116.5 1.03
IC C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0
IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0
IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212
IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284
IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0
IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0
IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0
IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0
IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0
IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0
PATCH FIRST URA5 LAST URA3
RESI THY -1.0 ! note: this is DNA,resname DT in ff14SB & ff99SB
GROUP
ATOM P P 1.1659
ATOM O1P O2 -0.7761 ! note: name is OP1 in ff14SB, O1P in ff99SB
ATOM O2P O2 -0.7761 ! note: name is OP2 in ff14SB, O2P in ff99SB
ATOM O5' OS -0.4954
GROUP
ATOM C5' CI -0.0069 ! type changed from CT (ff99SB) to CI (ff14SB)
ATOM H5' H1 0.0754 ! name is H5'1 in ff99SB
ATOM H5'' H1 0.0754 ! name is H5'2 in ff99SB
GROUP
ATOM C4' CT 0.1629
ATOM H4' H1 0.1176
ATOM O4' OS -0.3691
GROUP
ATOM C1' CT 0.0680
ATOM H1' H2 0.1804
ATOM N1 NG -0.0239 ! type is N* in ff14SB & ff99SB
GROUP
ATOM C6 CM -0.2209
ATOM H6 H4 0.2607
GROUP
ATOM C7 CT -0.2269
ATOM H71 HC 0.0770
ATOM H72 HC 0.0770
ATOM H73 HC 0.0770
GROUP
ATOM C4 C 0.5194
ATOM O4 O -0.5563
ATOM C5 CM 0.0025
GROUP
ATOM N3 NA -0.4340
ATOM H3 H 0.3420
GROUP
ATOM C2 C 0.5677
ATOM O2 O -0.5881
GROUP
ATOM C3' CT 0.0713
ATOM H3' H1 0.0985
ATOM O3' OS -0.5232
GROUP
ATOM C2' CT -0.0854
ATOM H2' HC 0.0718 ! name is H2'1 in ff99SB
ATOM H2'' HC 0.0718 ! name is H2'2 in ff99SB
! bonds from charmm (top_all22_na.inp)
! swapped C5M with C7
! swapped H5? with H7?
BOND P O1P P O2P P O5'
BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1'
BOND C1' N1 C1' C2' N1 C2 N1 C6 C2 O2
BOND C2 N3 N3 H3 N3 C4 C4 O4 C4 C5
BOND C5 C7 C5 C6 C2' C3' C3' O3' O3' +P
BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5'
BOND C5' H5'' C6 H6 C7 H71 C7 H72 C7 H73
BOND C2' H2'
IMPROPER C2 C6 N1 C1'
IMPROPER C4 C6 C5 C7
IMPROPER N1 N3 C2 O2
IMPROPER C5 N3 C4 O4
IMPROPER C2 C4 N3 H3
IMPROPER N1 C5 C6 H6
DONO H3 N3
ACCE O2 C2
ACCE O4 C4
ACCE O1P P
ACCE O2P P
ACCE O3'
ACCE O4'
ACCE O5'
! build from charmm (top_all36_na.rtf)
! name swapping as above, delete references to O2'
IC -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha
IC -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802
IC -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801
IC P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta
IC O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284
IC C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212
IC C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001
IC C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996
IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160
IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212
IC C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251
IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896
IC O4' C1' N1 C2 1.5251 113.71 -97.2 125.59 1.3783 !chi
IC C1' C2 *N1 C6 1.4896 117.06 -179.96 122.08 1.3704
IC C2 N1 C6 C5 1.3746 122.08 -0.02 121.23 1.3432
IC C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813
IC N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191
IC N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795
IC C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327
IC C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900
IC C4 C6 *C5 C7 1.4439 120.78 -179.94 121.63 1.5000
IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0
IC C6 C5 C7 H71 0.0 0.0 0.0 0.0 0.0
IC C5 H71 *C7 H72 0.0 0.0 115.0 0.0 0.0
IC H71 H72 *C7 H73 0.0 0.0 -115.0 0.0 0.0
IC C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0 !kept from Klauda's f99sb rtf file
IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0
IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0
IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0
IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0
IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0
IC C4' O5' *C5' H5'' 0.0 0. 115.0 0.0 0.0
PATCH FIRST THY5 LAST THY3
RESI CYT -1.0 ! note: this is RNA, resname C in ff14SB, RC in ff99SB
GROUP
ATOM P P 1.1662
ATOM O1P O2 -0.7760 ! name is OP1 in ff14SB, O1P in ff99SB
ATOM O2P O2 -0.7760 ! name is OP2 in ff14SB, O2P in ff99SB
ATOM O5' OS -0.4989
GROUP
ATOM C5' CI 0.0558 ! type changed from CT (ff99SB) to CI (ff14SB)
ATOM H5' H1 0.0679 ! name is H5'1 in ff99SB
ATOM H5'' H1 0.0679 ! name is H5'2 in ff99SB
GROUP
ATOM C4' CT 0.1065
ATOM H4' H1 0.1174
ATOM O4' OS -0.3548
GROUP
ATOM C1' CT 0.0066
ATOM H1' H2 0.2029
ATOM N1 NG -0.0484 ! name is type N* in ff14SB & ff99SB
GROUP
ATOM C6 C4 0.0053 ! type changed from CM (ff99SB) to C4 (ff14SB)
ATOM H6 H4 0.1958
GROUP
ATOM C5 C4 -0.5215 ! type changed from CM (ff99SB) to C4 (ff14SB)
ATOM H5 HA 0.1928
GROUP
ATOM N4 N2 -0.9530
ATOM H41 H 0.4234
ATOM H42 H 0.4234
ATOM C4 CA 0.8185
GROUP
ATOM C2 C 0.7538
ATOM O2 O -0.6252
ATOM N3 NC -0.7584
GROUP
ATOM C3' CT 0.2022
ATOM H3' H1 0.0615
ATOM O3' OS -0.5246
GROUP
ATOM C2' CT 0.0670
ATOM H2'' H1 0.0972 ! name is H2' in ff14SB, H2'1 in ff99SB
GROUP
ATOM O2' OH -0.6139
ATOM H2' HO 0.4186 ! name is HO2' in ff14SB, HO'2 in ff99SB
BOND P O1P P O2P P O5'
BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1'
BOND C1' N1 C1' C2' N1 C2 N1 C6 C2 O2
BOND C2 N3 N3 C4 C4 N4 N4 H41 N4 H42
BOND C4 C5 C5 C6 C2' C3' C3' O3' O3' +P
BOND C2' O2' O2' H2'
BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5'
BOND C5' H5'' C5 H5 C6 H6
IMPROPER C2 C6 N1 C1'
IMPROPER N1 N3 C2 O2
IMPROPER C4 H41 N4 H42
IMPROPER N1 C5 C6 H6
IMPROPER C6 C4 C5 H5
IMPROPER C5 N4 C4 N3
DONO H42 N4
DONO H2' O2'
DONO H41 N4
ACCE O2 C2
ACCE N3
ACCE O1P P
ACCE O2P P
ACCE O2'
ACCE O3'
ACCE O4'
ACCE O5'
! build array from charmm (top_all36_na.rtf)
IC -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha
IC -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802
IC -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801
IC P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta
IC O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284 !gamma
IC C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212 !delta
IC C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001 !epsilon
IC C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996 !zeta
IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160
IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212
IC C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251
IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896
IC O4' C1' N1 C2 1.5251 113.71 -97.2 125.59 1.3783 !chi
IC C1' C2 *N1 C6 1.4896 117.79 -180.00 120.6 1.364
IC C2 N1 C6 C5 1.399 120.6 0.0 121.0 1.337
IC C6 N1 C2 N3 1.364 120.6 0.0 118.9 1.356
IC N1 N3 *C2 O2 1.399 118.9 180.0 121.9 1.237
IC N1 C2 N3 C4 1.399 118.9 0.0 120.0 1.334
IC C5 N3 *C4 N4 1.426 121.8 180.00 118.9 1.337
IC N3 C4 N4 H41 1.337 117.9 0.00 118.9 1.01
IC H41 C4 *N4 H42 1.01 118.9 180.00 120.7 1.01
IC C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0
IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0
IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212
IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284
IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0
IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0
IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0
IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0
IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0
IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0
PATCH FIRST CYT5 LAST CYT3
RESI GUA -1.0 ! note: this is RNA, resname G in ff14SB, RG in ff99SB
GROUP
ATOM P P 1.1662
ATOM O1P O2 -0.7760 ! name is OP1 in ff14SB, O1P in ff99SB
ATOM O2P O2 -0.7760 ! name is OP2 in ff14SB, O2P in ff99SB
ATOM O5' OS -0.4989
GROUP
ATOM C5' CI 0.0558 ! type changed from CT (ff99SB) to CI (ff14SB)
ATOM H5' H1 0.0679 ! name is H5'1 in ff99SB
ATOM H5'' H1 0.0679 ! name is H5'2 in ff99SB
GROUP
ATOM C4' CT 0.1065
ATOM H4' H1 0.1174
ATOM O4' OS -0.3548
GROUP
ATOM C1' CT 0.0191
ATOM H1' H2 0.2006
ATOM N9 NG 0.0492 ! type is N* in ff14SB & ff99SB
GROUP
ATOM C8 CP 0.1374 ! type changed from CK (ff99SB) to CP (ff14SB)
ATOM H8 H5 0.1640
ATOM N7 NB -0.5709
GROUP
ATOM C6 C 0.4770
ATOM O6 O -0.5597
ATOM C5 CB 0.1744
GROUP
ATOM N1 NA -0.4787
ATOM H1 H 0.3424
GROUP
ATOM N2 N2 -0.9672
ATOM H21 H 0.4364
ATOM H22 H 0.4364
ATOM C2 CA 0.7657
GROUP
ATOM N3 NC -0.6323
ATOM C4 CB 0.1222
GROUP
ATOM C3' CT 0.2022
ATOM H3' H1 0.0615
ATOM O3' OS -0.5246
GROUP
ATOM C2' CT 0.0670
ATOM H2'' H1 0.0972 ! name is H2' in ff14SB, H2'1 in ff99SB
GROUP
ATOM O2' OH -0.6139
ATOM H2' HO 0.4186 ! name is HO2' in ff14SB, HO'2 in ff99SB
! bonds from charmm (top_all22_na.inp)
BOND P O1P P O2P P O5'
BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1'
BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3
BOND C4 C5 N3 C2 C2 N2 C2 N1 N2 H21
BOND N2 H22 N1 H1 N1 C6 C6 O6 C6 C5
BOND C5 N7 N7 C8 C2' C3' C3' O3' O3' +P
BOND C2' O2' O2' H2'
BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5'
BOND C5' H5'' C8 H8
IMPROPER C4 C8 N9 C1'
IMPROPER C5 N1 C6 O6
IMPROPER C6 C2 N1 H1
IMPROPER C2 H21 N2 H22
IMPROPER N7 N9 C8 H8
IMPROPER N2 N1 C2 N3
DONO H21 N2
DONO H22 N2
DONO H1 N1
DONO H2' O2'
ACCE O6 C6
ACCE N3
ACCE N7
ACCE O1P P
ACCE O2P P
ACCE O2'
ACCE O3'
ACCE O4'
ACCE O5'
! build array from charmm (top_all36_na.rtf)
! Chi and sugar-phosphate backbone in B-DNA like conformation (top_all36_na.rtf)
IC -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha
IC -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802
IC -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801
IC P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta
IC O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284 !gamma
IC C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212 !delta
IC C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001 !epsilon
IC C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996 !zeta
IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160
IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212
IC C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251 !puck
IC C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896
IC O4' C1' N9 C4 1.5251 113.71 -97.2 125.59 1.3783 !chi
IC C1' C4 *N9 C8 1.4896 125.59 -179.99 106.0 1.374
IC C4 N9 C8 N7 1.377 106.0 0.0 113.5 1.304
IC C8 N9 C4 C5 1.374 106.0 0.0 105.6 1.377
IC N9 C5 *C4 N3 1.377 105.6 180.0 128.4 1.355
IC C5 C4 N3 C2 1.377 128.4 0.0 111.8 1.327
IC C4 N3 C2 N1 1.355 111.8 0.0 124.0 1.375
IC N1 N3 *C2 N2 1.375 124.0 180.0 119.7 1.341
IC N3 C2 N2 H21 1.327 119.7 180.0 127.0 1.01
IC H21 C2 *N2 H22 1.01 127.0 -180.0 116.5 1.01
IC N3 C2 N1 C6 1.327 124.0 0.0 124.9 1.393
IC C6 C2 *N1 H1 1.393 124.9 180.0 117.4 1.03
IC C5 N1 *C6 O6 1.415 111.7 180.0 120.0 1.239
IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0
IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212
IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284
IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0
IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0
IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0
IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0
IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0
IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0
PATCH FIRST GUA5 LAST GUA3
!
! PROTEIN RESIDUES
!
RESI ALA 0.00
GROUP
ATOM N N -0.41570 ! |
ATOM HN H 0.27190 ! HN-N
GROUP
ATOM CA CX 0.03370 ! | HB1
ATOM HA H1 0.08230 ! | /
GROUP
ATOM CB CT -0.18250 ! HA-CA--CB-HB2 ALANINE
ATOM HB1 HC 0.06030 ! | \
ATOM HB2 HC 0.06030 ! | HB2
ATOM HB3 HC 0.06030 ! O=C
GROUP
ATOM C C 0.59730 ! |
ATOM O O -0.56790
BOND CB CA N HN N CA C CA C +N
BOND CA HA CB HB1 CB HB2 CB HB3 C O
IMPROPER -C CA N HN
IMPROPER CA +N C O
DONOR HN N
ACCEPTOR O C
IC -C CA *N HN 1.3551 126.4900 180.0000 115.4200 0.9996
IC -C N CA C 1.3551 126.4900 180.0000 114.4400 1.5390
IC N CA C +N 1.4592 114.4400 180.0000 116.8400 1.3558
IC +N CA *C O 1.3558 116.8400 180.0000 122.5200 1.2297
IC CA C +N +CA 1.5390 116.8400 180.0000 126.7700 1.4613
IC N C *CA CB 1.4592 114.4400 123.2300 111.0900 1.5461
IC N C *CA HA 1.4592 114.4400 -120.4500 106.3900 1.0840
IC C CA CB HB1 1.5390 111.0900 177.2500 109.6000 1.1109
IC HB1 CA *CB HB2 1.1109 109.6000 119.1300 111.0500 1.1119
IC HB1 CA *CB HB3 1.1109 109.6000 -119.5800 111.6100 1.1114
PATCH FIRST NALA LAST CALA
RESI ARG 1.00
GROUP
ATOM N N -0.34790 ! | HH11
ATOM HN H 0.27470 ! HN-N |
GROUP
ATOM CA CX -0.26370 ! | HB1 HG1 HD1 HE NH1-HH12
ATOM HA H1 0.15600 ! | | | | | //(+)
GROUP
ATOM CB C8 -0.00070 ! HA-CA--CB--CG--CD--NE--CZ
ATOM HB1 HC 0.03270 ! | | | | \
ATOM HB2 HC 0.03270 ! | HB2 HG2 HD2 NH2-HH22
GROUP
ATOM CG C8 0.03900 ! O=C |
ATOM HG1 HC 0.02850 ! | HH21
ATOM HG2 HC 0.02850