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top_amber2charmm.inp
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* 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
*
23 1
!
! 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,
! parm94.dat, all_nuc94.in, and all_amino* naming conventions
! where possible. Exceptions to this rule include types with "*"
! in the name (i.e. N*->NS, C*->CS). CHARMM atom names are utilized.
! 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 ~0.00005 using both CHARMM and AMBER. The AMBER energies
! and forces were calculated using AMBER 4.1/5.0_alpha sander
! (minimization or dynamics) and CHARMM c25n3 (ener). 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 carnal).
!
! 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...
! (3) The atom order is different for HIP, HID and HIE (all the
! histidine residues so force comparisons were only cursorly
! done, hence use these parameters at own risk. The energies
! agreed though!
! (4) TRP: the impropers on "CD1 CD2 CG CB" are giving a slight
! energy and force error that I do not understand at present.
! Use at own risk.
!
! Any problems? Let me know...
! cheatham@helix.nih.gov, cheatham@cgl.ucsf.edu
!
!
! AMBER atom types and masses (from all_nuc94.in)
!
MASS 1 BR 79.90 Br ! bromine
MASS 2 C 12.01 C ! sp2 C carbonyl group
MASS 3 CA 12.01 C ! sp2 C pure aromatic (benzene)
MASS 4 CB 12.01 C ! sp2 aromatic C, 5&6 membered ring junction
MASS 5 CC 12.01 C ! sp2 aromatic C, 5 memb. ring HIS
MASS 6 CK 12.01 C ! sp2 C 5 memb.ring in purines
MASS 7 CM 12.01 C ! sp2 C pyrimidines in pos. 5 & 6
MASS 8 CN 12.01 C ! sp2 C aromatic 5&6 memb.ring junct.(TRP)
MASS 9 CQ 12.01 C ! sp2 C in 5 mem.ring of purines between 2 N
MASS 10 CR 12.01 C ! sp2 arom as CQ but in HIS
MASS 11 CT 12.01 C ! sp3 aliphatic C
MASS 12 CV 12.01 C ! sp2 arom. 5 memb.ring w/1 N and 1 H (HIS)
MASS 13 CW 12.01 C ! sp2 arom. 5 memb.ring w/1 N-H and 1 H (HIS)
MASS 14 CS 12.01 C ! sp2 arom. 5 memb.ring w/1 subst. (TRP)
MASS 15 C0 40.08 C ! calcium
MASS 16 H 1.008 H ! H bonded to nitrogen atoms
MASS 17 HC 1.008 H ! H aliph. bond. to C without electrwd.group
MASS 18 H1 1.008 H ! H aliph. bond. to C with 1 electrwd. group
MASS 19 H2 1.008 H ! H aliph. bond. to C with 2 electrwd.groups
MASS 20 H3 1.008 H ! H aliph. bond. to C with 3 eletrwd.groups
MASS 21 HA 1.008 H ! H arom. bond. to C without elctrwd. groups
MASS 22 H4 1.008 H ! H arom. bond. to C with 1 electrwd. group
MASS 23 H5 1.008 H ! H arom. bond. to C with 2 electrwd. groups
MASS 24 HO 1.008 H ! hydroxyl group
MASS 25 HS 1.008 H ! hydrogen bonded to sulphur
MASS 26 HW 1.008 H ! H in TIP3P water
MASS 27 HP 1.008 H ! H bonded to C next to positively charged gr
MASS 28 F 19.00 F ! fluorine
MASS 29 I 126.9 I ! iodine
MASS 30 IM 35.45 Cl ! assumed to be Cl-
MASS 31 IP 22.99 Na ! assumed to be Na+
MASS 32 IB 131.0 XX ! 'big ion w/ waters' for vacuum (Na+, 6H2O)
MASS 33 MG 24.305 Mg ! magnesium
MASS 34 N 14.01 N ! sp2 nitrogen in amide groups
MASS 35 NA 14.01 N ! sp2 N in 5 memb.ring w/H atom (HIS)
MASS 36 NB 14.01 N ! sp2 N in 5 memb.ring w/LP (HIS,ADE,GUA)
MASS 37 NC 14.01 N ! sp2 N in 6 memb.ring w/LP (ADE,GUA)
MASS 38 N2 14.01 N ! sp2 N in amino groups
MASS 39 N3 14.01 N ! sp3 N for charged amino groups (Lys, etc)
MASS 40 NS 14.01 N ! sp2 N; note N* --> NS to avoid confusion with wildcard
MASS 41 O 16.00 O ! carbonyl group oxygen
MASS 42 OW 16.00 O ! oxygen in TIP3P water
MASS 43 OH 16.00 O ! oxygen in hydroxyl group
MASS 44 OS 16.00 O ! ether and ester oxygen
MASS 45 O2 16.00 O ! carboxyl and phosphate group oxygen
MASS 46 P 30.97 P ! phosphate
MASS 47 S 32.06 S ! sulphur in disulfide linkage
MASS 48 SH 32.06 S ! sulphur in cystine
MASS 49 CU 63.55 Cu ! copper
MASS 50 FE 55.00 Fe ! iron
MASS 51 Li 6.94 Li ! lithium
MASS 52 K 39.10 K ! potassium
MASS 53 Rb 85.47 Rb ! rubidium
! new mass
MASS 54 nh 14.01 nh !ligand
MASS 55 cg 12.01 cg !ligand
MASS 56 n1 14.01 n1 !ligand
MASS 57 hc 1.008 hc !ligand
MASS 58 nd 14.01 nd !ligand
MASS 59 cd 12.01 cd !ligand
MASS 60 h1 1.008 h1 !ligand
MASS 61 oh 16.0 oh !ligand
MASS 62 h4 1.008 h4 !ligand
MASS 63 ca 12.01 ca !ligand
MASS 64 ha 1.008 ha !ligand
MASS 65 na 14.01 na !ligand
MASS 66 cc 12.01 cc !ligand
MASS 67 ho 1.008 ho !ligand
MASS 68 nc 14.01 nc !ligand
MASS 69 c3 12.01 c3 !ligand
MASS 70 hn 1.008 hn !ligand
! ligand K109
MASS 100 nb 14.01 nb !ligand
MASS 101 cl 35.45 cl !ligand
MASS 62 os 16.0 os !ligand
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
RESI K49 0.0
GROUP
ATOM C5 ca 0.0529446826015
ATOM C17 cd 0.0318220165203
ATOM C16 cc -0.341487102086
ATOM N4 na 0.0148988805159
ATOM N5 nd -0.274087594951
ATOM H7 hc 0.0650162063666
ATOM C4 ca -0.127763126235
ATOM H12 h1 0.0741213556531
ATOM H17 h4 0.186657559824
ATOM H13 hc 0.071160981888
ATOM N1 n1 -0.375106345774
ATOM C14 c3 0.123144543359
ATOM H15 ha 0.161521386937
ATOM C1 cg 0.23945522393
ATOM C7 ca -0.0870609890231
ATOM C15 c3 -0.14359412404
ATOM H8 hc 0.067714546652
ATOM C6 ca -0.143495111965
ATOM H10 h1 0.0728581959385
ATOM C8 cc -0.178101479693
ATOM H16 h4 0.183068106476
ATOM N3 nh -0.833622217344
ATOM H1 ha 0.141347840834
ATOM H6 h1 0.0891752557629
ATOM C2 ca -0.0347023800768
ATOM C12 c3 -0.121150291438
ATOM H4 ha 0.141950917124
ATOM C11 c3 0.21074559989
ATOM H11 h1 0.0201445426454
ATOM H9 h1 0.0208016255763
ATOM C18 cc -0.0965471860593
ATOM H14 hc 0.0686176608123
ATOM C10 cc 0.685646542261
ATOM H2 ha 0.154446493963
ATOM C9 cd 0.428930138858
ATOM H5 hn 0.416075516465
ATOM H3 ha 0.13574413337
ATOM C13 c3 0.122645480241
ATOM C3 ca -0.0888122096597
ATOM N2 nd -0.723135274424
ATOM O1 os -0.411988000549
BOND C3 H1
BOND C4 H2
BOND C6 H3
BOND C7 H4
BOND N3 H5
BOND C11 H6
BOND C12 H7
BOND C12 H8
BOND C13 H9
BOND C13 H10
BOND C14 H11
BOND C14 H12
BOND C15 H13
BOND C15 H14
BOND C16 H15
BOND C17 H16
BOND C18 H17
BOND N1 C1
BOND C1 C2
BOND C2 C3
BOND C2 C7
BOND C3 C4
BOND C4 C5
BOND C5 C6
BOND C5 C8
BOND C6 C7
BOND C8 C9
BOND C8 C18
BOND C9 N2
BOND C9 N4
BOND N2 C10
BOND C10 N3
BOND C10 C16
BOND N3 C11
BOND C11 C12
BOND C11 C15
BOND C12 C13
BOND C13 O1
BOND O1 C14
BOND C14 C15
BOND C16 C17
BOND C17 N4
BOND N4 N5
BOND N5 C18
RESI K51 0.0
GROUP
ATOM N4 n1 -0.36591618551
ATOM C13 cg 0.23496265697
ATOM C10 ca -0.0209786479144
ATOM C11 ca -0.0904494165752
ATOM C12 ca -0.12559485236
ATOM C7 ca 0.0305998622942
ATOM C8 ca -0.115240545554
ATOM C5 cc -0.0803621432492
ATOM C9 ca -0.0940888759605
ATOM C6 cd -0.126553973655
ATOM N3 nd -0.114802490121
ATOM C1 cc -0.10076971899
ATOM C2 cc -0.0211846739297
ATOM C3 cd -0.263768292536
ATOM C4 cd 0.61330740944
ATOM N1 nc -0.562610010977
ATOM N5 nh -0.806729824369
ATOM N2 na 0.188680815038
ATOM C14 c3 0.20591599067
ATOM C15 c3 0.0931097524698
ATOM C16 c3 -0.0679005702525
ATOM O1 oh -0.61163819978
ATOM C17 c3 -0.0851707502744
ATOM C18 c3 -0.0931887623491
ATOM H11 ha 0.14641648079
ATOM H12 ha 0.144943294731
ATOM H8 ha 0.150058940176
ATOM H9 ha 0.143044054885
ATOM H6 h4 0.185817453897
ATOM H2 ha 0.170362502744
ATOM H3 ha 0.156423743688
ATOM HN5 hn 0.420668096048
ATOM H14 h1 0.0872220093304
ATOM H151 h1 0.0373527145993
ATOM H152 h1 0.0378837816685
ATOM H16 hc 0.0654372596048
ATOM HO1 ho 0.407556441273
ATOM H171 hc 0.03404929764
ATOM H172 hc 0.0420463070252
ATOM H173 hc 0.037772767618
ATOM H181 hc 0.042228330022
ATOM H182 hc 0.0331921894621
ATOM H183 hc 0.037896783315
BOND C11 H11
BOND C12 H12
BOND C8 H8
BOND C9 H9
BOND C6 H6
BOND C2 H2
BOND C3 H3
BOND N5 HN5
BOND C14 H14
BOND C15 H151
BOND C15 H152
BOND C16 H16
BOND O1 HO1
BOND C17 H171
BOND C17 H172
BOND C17 H173
BOND C18 H181
BOND C18 H182
BOND C18 H183
BOND N4 C13
BOND C13 C10
BOND C10 C11
BOND C10 C9
BOND C11 C12
BOND C12 C7
BOND C7 C8
BOND C7 C5
BOND C8 C9
BOND C5 C6
BOND C5 N2
BOND C6 N3
BOND N3 C1
BOND C1 C2
BOND C1 N2
BOND C2 C3
BOND C3 C4
BOND C4 N1
BOND C4 N5
BOND N1 N2
BOND N5 C14
BOND C14 C15
BOND C14 C16
BOND C15 O1
BOND C16 C17
BOND C16 C18
IMPR C11 C7 C12 H12
IMPR C7 C9 C8 H8
IMPR C10 C8 C9 H9
IMPR C5 H6 C6 N3
IMPR C1 C3 C2 H2
IMPR C2 C4 C3 H3
IMPR C14 C4 N5 HN5
IMPR C11 C9 C10 C13
IMPR C12 C8 C7 C5
IMPR C7 C6 C5 N2
IMPR C2 N2 C1 N3
IMPR C3 N1 C4 N5
IMPR C5 C1 N2 N1
RESI K10 0.0
GROUP
ATOM H8 ha 0.149344850165
ATOM N2 nh -0.842744368825
ATOM H9 ha 0.147407605379
ATOM H6 h1 0.0491382021954
ATOM H13 h4 0.181806947311
ATOM H2 ha 0.150600008782
ATOM Cl1 cl -0.102359919868
ATOM C2 ca -0.124171672887
ATOM H14 h4 0.185857458836
ATOM H1 ha 0.14396417124
ATOM C16 cc -0.339677873765
ATOM C8 cd 0.421484199232
ATOM H3 ha 0.13370187596
ATOM C10 c3 0.25081165697
ATOM H11 h4 0.0259852798573
ATOM H10 h4 0.0257672523052
ATOM H7 h1 0.0848797135016
ATOM C4 ca 0.0247551245884
ATOM N3 nb -0.662751652031
ATOM N5 nd -0.275369756861
ATOM C6 ca -0.122480459385
ATOM C9 cc 0.678738671789
ATOM H12 ha 0.160717285401
ATOM C3 ca -0.110105897366
ATOM C12 ca -0.0753355087816
ATOM C11 ca -0.231111170692
ATOM C1 ca 0.00947519593853
ATOM N4 na 0.0149028810099
ATOM C13 ca -0.248431356751
ATOM C15 ca 0.407128387486
ATOM C5 ca -0.126017905598
ATOM H5 hn 0.422766361142
ATOM H4 ha 0.144312215148
ATOM C14 ca 0.401481674533
ATOM N1 nd -0.71940280461
ATOM C7 cc -0.164105713502
ATOM C17 cd 0.0304558441273
ATOM C18 cc -0.101417800768
BOND C2 H1
BOND C3 H2
BOND C5 H3
BOND C6 H4
BOND N2 H5
BOND C10 H6
BOND C10 H7
BOND C12 H8
BOND C13 H9
BOND C14 H10
BOND C15 H11
BOND C16 H12
BOND C17 H13
BOND C18 H14
BOND Cl1 C1
BOND C1 C2
BOND C1 C6
BOND C2 C3
BOND C3 C4
BOND C4 C5
BOND C4 C7
BOND C5 C6
BOND C7 C8
BOND C7 C18
BOND C8 N1
BOND C8 N4
BOND N1 C9
BOND C9 N2
BOND C9 C16
BOND N2 C10
BOND C10 C11
BOND C11 C12
BOND C11 C15
BOND C12 C13
BOND C13 C14
BOND C14 N3
BOND N3 C15
BOND C16 C17
BOND C17 N4
BOND N4 N5
BOND N5 C18
RESIDUE ADE -1.0 ! note: this is RNA (RA); patches to make
GROUP ! terminal or deoxyribose are required
ATOM P P 1.1662
ATOM O1P O2 -0.7760
ATOM O2P O2 -0.7760
ATOM O5' OS -0.4989
ATOM C5' CT 0.0558
ATOM H5' H1 0.0679 ! note: type is H5'1 --> this should be checked
ATOM H5'' H1 0.0679 ! note: type is H5'2
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 NS -0.0251 ! note: type is N*
ATOM C8 CK 0.2006
ATOM H8 H5 0.1553
ATOM N7 NB -0.6073
ATOM C5 CB 0.0515
ATOM C6 CA 0.7009
ATOM N6 N2 -0.9019
ATOM H61 H 0.4115
ATOM H62 H 0.4115
ATOM N1 NC -0.7615
ATOM C2 CQ 0.5875
ATOM H2 H5 0.0473
ATOM N3 NC -0.6997
ATOM C4 CB 0.3053
ATOM C3' CT 0.2022
ATOM H3' H1 0.0615
ATOM C2' CT 0.0670
ATOM H2'' H1 0.0972 ! note: this is H2'1
ATOM O2' OH -0.6139
ATOM H2' HO 0.4186 ! note: this is HO'2
ATOM O3' OS -0.5246
! 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 C8 C4 N9 C1'
IMPROPER C6 H61 N6 H62
IMPROPER N7 N9 C8 H8
IMPROPER N1 N3 C2 H2
IMPROPER C5 N1 C6 N6
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'
! using charmm geometry (top_all22_na.inp)
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' N9 1.5284 101.97 144.39 113.71 1.4896
IC O4' C1' N9 C4 1.5251 113.71 -96.00 125.97 1.3703
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
RESIDUE URA -1.0 ! note: this is RNA (RA); patches to make
GROUP ! terminal are required.
ATOM P P 1.1662
ATOM O1P O2 -0.7760
ATOM O2P O2 -0.7760
ATOM O5' OS -0.4989
ATOM C5' CT 0.0558
ATOM H5' H1 0.0679 ! note: name is H5'1
ATOM H5'' H1 0.0679 ! note: name is H5'2
ATOM C4' CT 0.1065
ATOM H4' H1 0.1174
ATOM O4' OS -0.3548
ATOM C1' CT 0.0674
ATOM H1' H2 0.1824
ATOM N1 NS 0.0418 ! note: type is N*
ATOM C6 CM -0.1126
ATOM H6 H4 0.2188
ATOM C5 CM -0.3635
ATOM H5 HA 0.1811
ATOM C4 C 0.5952
ATOM O4 O -0.5761
ATOM N3 NA -0.3549
ATOM H3 H 0.3154
ATOM C2 C 0.4687
ATOM O2 O -0.5477
ATOM C3' CT 0.2022
ATOM H3' H1 0.0615
ATOM C2' CT 0.0670
ATOM H2'' H1 0.0972 ! note: name is H2'1
ATOM O2' OH -0.6139
ATOM H2' HO 0.4186 ! note: name is HO'2
ATOM O3' OS -0.5246
! 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 C6 C2 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 from charmm (top_all22_na.inp)
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
RESIDUE THY -1.0 ! note: this is DNA (DT); patches to make
GROUP ! terminal are required
ATOM P P 1.1659
ATOM O1P O2 -0.7761
ATOM O2P O2 -0.7761
ATOM O5' OS -0.4954
ATOM C5' CT -0.0069
ATOM H5' H1 0.0754 ! this is H5'1
ATOM H5'' H1 0.0754 ! this is H5'2
ATOM C4' CT 0.1629
ATOM H4' H1 0.1176
ATOM O4' OS -0.3691
ATOM C1' CT 0.0680
ATOM H1' H2 0.1804
ATOM N1 NS -0.0239 ! this is atom type N*
ATOM C6 CM -0.2209
ATOM H6 H4 0.2607
ATOM C5 CM 0.0025
ATOM C7 CT -0.2269
ATOM H71 HC 0.0770
ATOM H72 HC 0.0770
ATOM H73 HC 0.0770
ATOM C4 C 0.5194
ATOM O4 O -0.5563
ATOM N3 NA -0.4340
ATOM H3 H 0.3420
ATOM C2 C 0.5677
ATOM O2 O -0.5881
ATOM C3' CT 0.0713
ATOM H3' H1 0.0985
ATOM C2' CT -0.0854
ATOM H2' HC 0.0718 ! this is H2'1
ATOM H2'' HC 0.0718 ! this is H2'2
ATOM O3' OS -0.5232
! 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 C6 C2 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_all22_na.inp)
! name swapping as above, delete references to O2'
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 -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
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 0.0 115.0 0.0 0.0
PATCH FIRST THY5 LAST THY3
RESI CYT -1.0 ! note: this is RNA (RC); patches to make
GROUP ! terminal or deoxyribose are required
ATOM P P 1.1662
ATOM O1P O2 -0.7760
ATOM O2P O2 -0.7760
ATOM O5' OS -0.4989
ATOM C5' CT 0.0558
ATOM H5' H1 0.0679 ! this is H5'1
ATOM H5'' H1 0.0679 ! this is H5'2
ATOM C4' CT 0.1065
ATOM H4' H1 0.1174
ATOM O4' OS -0.3548
ATOM C1' CT 0.0066
ATOM H1' H2 0.2029
ATOM N1 NS -0.0484 ! this is type N*
ATOM C6 CM 0.0053
ATOM H6 H4 0.1958
ATOM C5 CM -0.5215
ATOM H5 HA 0.1928
ATOM C4 CA 0.8185
ATOM N4 N2 -0.9530
ATOM H41 H 0.4234
ATOM H42 H 0.4234
ATOM N3 NC -0.7584
ATOM C2 C 0.7538
ATOM O2 O -0.6252
ATOM C3' CT 0.2022
ATOM H3' H1 0.0615
ATOM C2' CT 0.0670
ATOM H2'' H1 0.0972 ! this is H2'1
ATOM O2' OH -0.6139
ATOM H2' HO 0.4186 ! this is HO'2
ATOM O3' OS -0.5246
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 C6 C2 N1 C1'
IMPROPER N1 N3 C2 O2
IMPROPER C4 H41 N4 H42
IMPROPER N1 C5 C6 H6
IMPROPER C6 C4 C5 H5
IMPROPER N3 C5 C4 N4
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'
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 -96.0 117.79 1.399
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 GUA (RG); patches to make
GROUP ! terminal or deoxyribose are required
ATOM P P 1.1662
ATOM O1P O2 -0.7760
ATOM O2P O2 -0.7760
ATOM O5' OS -0.4989
ATOM C5' CT 0.0558
ATOM H5' H1 0.0679 ! this is H5'1
ATOM H5'' H1 0.0679 ! this is H5'2
ATOM C4' CT 0.1065
ATOM H4' H1 0.1174
ATOM O4' OS -0.3548
ATOM C1' CT 0.0191
ATOM H1' H2 0.2006
ATOM N9 NS 0.0492 ! this is type N*
ATOM C8 CK 0.1374
ATOM H8 H5 0.1640
ATOM N7 NB -0.5709
ATOM C5 CB 0.1744
ATOM C6 C 0.4770
ATOM O6 O -0.5597
ATOM N1 NA -0.4787
ATOM H1 H 0.3424
ATOM C2 CA 0.7657
ATOM N2 N2 -0.9672
ATOM H21 H 0.4364
ATOM H22 H 0.4364
ATOM N3 NC -0.6323
ATOM C4 CB 0.1222
ATOM C3' CT 0.2022
ATOM H3' H1 0.0615
ATOM C2' CT 0.0670
ATOM H2'' H1 0.0972 ! this is H2'1
ATOM O2' OH -0.6139
ATOM H2' HO 0.4186 ! this is HO'2
ATOM O3' OS -0.5246
! 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 C8 C4 N9 C1'
IMPROPER C5 N1 C6 O6
IMPROPER C6 C2 N1 H1
IMPROPER C2 H21 N2 H22
IMPROPER N7 N9 C8 H8
IMPROPER N1 N3 C2 N2
DONO H21 N2
DONO H22 N2
DONO H1 N1
DONO H2' O2'
ACCE O6 C6
ACCE N3
ACCE N7
ACCE O1P P