[gmx-users] Error: number of atoms do not match
Tsjerk Wassenaar
tsjerkw at gmail.com
Thu Jul 10 20:27:03 CEST 2008
Hi Harshith,
The GROMOS96 force fields are united atom force fields, so it makes
sense to use the model without explicit non-polar hydrogens. However,
as you can see in the topology, the aromatic hydrogens are treated
explicitly.This is to allow for some charge separation, emulating the
negativity due to the electron density on both sides around the ring
center.
By the way, maybe you'd be better off making a styrene building block
and add it to the .rtp library, such that you can use pdb2gmx to
generate topologies for arbitrary length chains. Also, compare the
topology from PRODRG to the phenyl group from phenylalanine. That was
actually parameterized based on toluene, so it's pretty close to your
target.
Hope it helps,
Tsjerk
On Wed, Jul 9, 2008 at 2:02 PM, h a <y600100 at gmail.com> wrote:
> Dear Users,
>
> I used prodrg( gomos96.1) to generate topology and .gro files of polystyrene
> ( of 10 monomers ). the read me file is as shown
> *****
> DRGFIN.PDB : the final PDB file with all hydrogens added
> DRGPOH.PDB : the final PDB file with only polar hydrogens added
> DRGNOH.PDB : the final PDB file without any hydrogens added
>
> DRGFIN.MOL : the final Molfile with all hydrogens added
> DRGPOH.MOL : the final Molfile with only polar hydrogens added
> DRGNOH.MOL : the final Molfile without any hydrogens added
>
> DRGFIN.GRO : final coordinates in GROMOS87 format (all hydrogens)
> DRGPOH.GRO : final coordinates in GROMOS87 format (polar hydrogens only)
>
> DRGCNS.PAR : CNS parameter file
> DRGCNS.TOP : CNS topology file
>
> DRGMAC.LIB : REFMAC5 library
>
> DRGSHX.TOP : SHELX topology
>
> DRGTRS.O : O <9.0 torsion database (read in with: read DRGTRS.O in O)
> DRGFNOH.O6 : O <9.0 refi dictionary
> DRGNOH.O : O 9.x dictionary
>
> DRGGMX.ITP : GROMACS .itp file
>
> DRGWIF.TOP : WHAT IF topology
>
> DRGFIN.MOL2 : SYBYL2 file with all hydrogens
> DRGPOH.MOL2 : SYBYL2 file with only polar hydrogens
>
> DRGAD2.PDBQ : AutoDock 2.4 PDBQ file
> DRGAD3.PDBQ : AutoDock 3.0 PDBQ file
>
> DRGHEX.TOP : HEX topology
> *****************
>
> Now I'm actually studying protein polymer_surface interactions, using g43a1
> forcefield . Can anybody explain whether should I use polymer model with
> only polar hydrogens or polymer model with all hydrogens ? What is the
> significance of these hydrogens.
> In the .itp file(shown below) there are 130 atoms but total number of atoms
> in only polar hydrogens model is 80 same with no hydrogens model. Including
> all hydrogens I have 162 atoms. So what does this 130 correspond to ?? (
> actually I'm facing fatal error because of this consistency in number of
> atoms while doing EM )
> *******
> [ atoms ]
> ; nr type resnr resid atom cgnr charge mass
> 1 CR1 1 STY CAB 1 -0.006 12.0110
> 2 HC 1 STY HAB 1 0.006 1.0080
> 3 CR1 1 STY CAC 2 -0.016 12.0110
> 4 HC 1 STY HAC 2 0.002 1.0080
> 5 CR1 1 STY CAD 2 -0.017 12.0110
> 6 HC 1 STY HAD 2 0.002 1.0080
> 7 CR1 1 STY CAE 2 -0.017 12.0110
> 8 HC 1 STY HAE 2 0.002 1.0080
> 9 CR1 1 STY CAF 2 -0.017 12.0110
> 10 HC 1 STY HAF 2 0.002 1.0080
> 11 C 1 STY CAA 2 -0.025 12.0110
> 12 CH1 1 STY CAG 2 0.067 13.0190
> 13 CH3 1 STY CAH 2 0.017 15.0350
> 14 CH2 1 STY CAP 3 0.000 14.0270
> 15 CH1 1 STY CAO 4 0.060 13.0190
> 16 C 1 STY CAI 4 -0.027 12.0110
> 17 CR1 1 STY CAJ 4 -0.018 12.0110
> 18 HC 1 STY HAK 4 0.001 1.0080
> 19 CR1 1 STY CAK 4 -0.018 12.0110
> 20 HC 1 STY HAL 4 0.002 1.0080
> 21 CR1 1 STY CAL 5 -0.016 12.0110
> 22 HC 1 STY HAM 5 0.003 1.0080
> 23 CR1 1 STY CAM 5 -0.016 12.0110
> 24 HC 1 STY HAN 5 0.003 1.0080
> 25 CR1 1 STY CAN 5 -0.016 12.0110
> 26 HC 1 STY HAO 5 0.003 1.0080
> 27 CH2 1 STY CAX 5 0.039 14.0270
> 28 CH1 1 STY CAW 6 0.060 13.0190
> 29 C 1 STY CAQ 6 -0.027 12.0110
> 30 CR1 1 STY CAR 6 -0.018 12.0110
> 31 HC 1 STY HAS 6 0.001 1.0080
> 32 CR1 1 STY CAS 6 -0.018 12.0110
> 33 HC 1 STY HAT 6 0.002 1.0080
> 34 CR1 1 STY CAT 7 -0.016 12.0110
> 35 HC 1 STY HAU 7 0.003 1.0080
> 36 CR1 1 STY CAU 7 -0.016 12.0110
> 37 HC 1 STY HAV 7 0.003 1.0080
> 38 CR1 1 STY CAV 7 -0.016 12.0110
> 39 HC 1 STY HAW 7 0.003 1.0080
> 40 CH2 1 STY CBF 7 0.039 14.0270
> 41 CH1 1 STY CBE 8 0.060 13.0190
> 42 C 1 STY CAY 8 -0.027 12.0110
> 43 CR1 1 STY CAZ 8 -0.018 12.0110
> 44 HC 1 STY HA0 8 0.001 1.0080
> 45 CR1 1 STY CBA 8 -0.018 12.0110
> 46 HC 1 STY HBA 8 0.002 1.0080
> 47 CR1 1 STY CBB 9 -0.016 12.0110
> 48 HC 1 STY HBB 9 0.003 1.0080
> 49 CR1 1 STY CBC 9 -0.016 12.0110
> 50 HC 1 STY HBC 9 0.003 1.0080
> 51 CR1 1 STY CBD 9 -0.016 12.0110
> 52 HC 1 STY HBD 9 0.003 1.0080
> 53 CH2 1 STY CBN 9 0.039 14.0270
> 54 CH1 1 STY CBM 10 0.060 13.0190
> 55 C 1 STY CBG 10 -0.027 12.0110
> 56 CR1 1 STY CBH 10 -0.018 12.0110
> 57 HC 1 STY HBH 10 0.001 1.0080
> 58 CR1 1 STY CBI 10 -0.018 12.0110
> 59 HC 1 STY HBI 10 0.002 1.0080
> 60 CR1 1 STY CBJ 11 -0.016 12.0110
> 61 HC 1 STY HBJ 11 0.003 1.0080
> 62 CR1 1 STY CBK 11 -0.016 12.0110
> 63 HC 1 STY HBK 11 0.003 1.0080
> 64 CR1 1 STY CBL 11 -0.016 12.0110
> 65 HC 1 STY HBL 11 0.003 1.0080
> 66 CH2 1 STY CBV 11 0.039 14.0270
> 67 CH1 1 STY CBU 12 0.060 13.0190
> 68 C 1 STY CBO 12 -0.027 12.0110
> 69 CR1 1 STY CBP 12 -0.018 12.0110
> 70 HC 1 STY HBP 12 0.001 1.0080
> 71 CR1 1 STY CBQ 12 -0.018 12.0110
> 72 HC 1 STY HBQ 12 0.002 1.0080
> 73 CR1 1 STY CBR 13 -0.016 12.0110
> 74 HC 1 STY HBR 13 0.003 1.0080
> 75 CR1 1 STY CBS 13 -0.016 12.0110
> 76 HC 1 STY HBS 13 0.003 1.0080
> 77 CR1 1 STY CBT 13 -0.016 12.0110
> 78 HC 1 STY HBT 13 0.003 1.0080
> 79 CH2 1 STY CCD 13 0.039 14.0270
> 80 CH1 1 STY CCC 14 0.060 13.0190
> 81 C 1 STY CBW 14 -0.027 12.0110
> 82 CR1 1 STY CBX 14 -0.018 12.0110
> 83 HC 1 STY HBX 14 0.001 1.0080
> 84 CR1 1 STY CBY 14 -0.018 12.0110
> 85 HC 1 STY HBY 14 0.002 1.0080
> 86 CR1 1 STY CBZ 15 -0.016 12.0110
> 87 HC 1 STY HBZ 15 0.003 1.0080
> 88 CR1 1 STY CCA 15 -0.016 12.0110
> 89 HC 1 STY HCA 15 0.003 1.0080
> 90 CR1 1 STY CCB 15 -0.016 12.0110
> 91 HC 1 STY HCB 15 0.003 1.0080
> 92 CH2 1 STY CCL 15 0.039 14.0270
> 93 CH1 1 STY CCK 16 0.060 13.0190
> 94 C 1 STY CCE 16 -0.027 12.0110
> 95 CR1 1 STY CCF 16 -0.018 12.0110
> 96 HC 1 STY HCF 16 0.001 1.0080
> 97 CR1 1 STY CCG 16 -0.018 12.0110
> 98 HC 1 STY HCG 16 0.002 1.0080
> 99 CR1 1 STY CCH 17 -0.016 12.0110
> 100 HC 1 STY HCH 17 0.003 1.0080
> 101 CR1 1 STY CCI 17 -0.016 12.0110
> 102 HC 1 STY HCI 17 0.003 1.0080
> 103 CR1 1 STY CCJ 17 -0.016 12.0110
> 104 HC 1 STY HCJ 17 0.003 1.0080
> 105 CH2 1 STY CCT 17 0.039 14.0270
> 106 CH1 1 STY CCS 18 0.060 13.0190
> 107 C 1 STY CCM 18 -0.027 12.0110
> 108 CR1 1 STY CCN 18 -0.018 12.0110
> 109 HC 1 STY HCN 18 0.001 1.0080
> 110 CR1 1 STY CCO 18 -0.018 12.0110
> 111 HC 1 STY HCO 18 0.002 1.0080
> 112 CR1 1 STY CCP 19 -0.016 12.0110
> 113 HC 1 STY HCP 19 0.003 1.0080
> 114 CR1 1 STY CCQ 19 -0.016 12.0110
> 115 HC 1 STY HCQ 19 0.003 1.0080
> 116 CR1 1 STY CCR 19 -0.016 12.0110
> 117 HC 1 STY HCR 19 0.003 1.0080
> 118 CH2 1 STY CDB 19 0.039 14.0270
> 119 CH2 1 STY CDA 20 0.066 14.0270
> 120 C 1 STY CCU 20 -0.019 12.0110
> 121 CR1 1 STY CCV 20 -0.012 12.0110
> 122 HC 1 STY HCV 20 0.003 1.0080
> 123 CR1 1 STY CCW 20 -0.013 12.0110
> 124 HC 1 STY HCW 20 0.004 1.0080
> 125 CR1 1 STY CCX 20 -0.013 12.0110
> 126 HC 1 STY HCX 20 0.004 1.0080
> 127 CR1 1 STY CCY 20 -0.013 12.0110
> 128 HC 1 STY HCY 20 0.003 1.0080
> 129 CR1 1 STY CCZ 20 -0.013 12.0110
> 130 HC 1 STY HCZ 20 0.003 1.0080
>
> [ bonds ]
> ; ai aj fu c0, c1, ...
> 1 2 2 0.109 12300000.0 0.109 12300000.0 ; CAB HAB
> 1 3 2 0.139 10800000.0 0.139 10800000.0 ; CAB CAC
> .
> .
> .
> .
> .
> ************
>
> Thank you so much for your help :)
>
> Sincerely,
> Harshith, Under Graduate,
> IITK
> http://home.iitk.ac.in/~harshith
>
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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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