[gmx-users] how can I get a topology?

日産化学 石川誠 isikawam at nissanchem.co.jp
Thu Feb 23 02:44:26 CET 2006


1.copy a topology text result on prodrg/web site
2.save it as mymol.itp
3.copy it in the same directory as the topology file
4.add the following line in the topology file

; Include molecular topology file
#include "mymol.itp"

makoto

> -----Original Message-----
> From: gmx-users-bounces at gromacs.org 
> [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Yang Ye
> Sent: Thursday, February 23, 2006 10:28 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] how can I get a topology?
> 
> 
> After generating the molecule from PRODRG, it is not neede to 
> run pdb2gmx.
> 
> Yang Ye
> 
> Yegor Isakov wrote:
> > I need topology for this molecule - SH-CH=O
> > I made a pdb file through pymol, opened PRODRG site
> > (http://davapc1.bioch.dundee.ac.uk/programs/prodrg/prodrg.html), 
> > generated an itp file over there:
> > ;      
> > ;      
> > ;       This file was generated by PRODRG version 051202.0518
> > ;       PRODRG written/copyrighted by Daan van Aalten
> > ;      
> > ;       Questions/comments to dava at davapc1.bioch.dundee.ac.uk
> > ;      
> > ;       When using this software in a publication, cite:
> > ;       A. W. Schuettelkopf and D. M. F. van Aalten (2004).
> > ;       PRODRG - a tool for high-throughput crystallography
> > ;       of protein-ligand complexes.
> > ;       Acta Crystallogr. D60, 1355--1363.
> > ;      
> > ;      
> >
> > [ moleculetype ]
> > ; Name nrexcl
> > C=O      3
> >
> > [ atoms ]
> > ;   nr      type  resnr resid  atom  cgnr   charge     mass
> >      1         O     1  C=O     O02     1   -0.367  15.9994  
> >      2         C     1  C=O     C01     1    0.252  12.0110  
> >      3         S     1  C=O     S01     1    0.096  32.0600  
> >      4        HS     1  C=O     HAA     1    0.019   1.0080  
> >
> > [ bonds ]
> > ; ai  aj  fu    c0, c1, ...
> >    1   2   1    0.123    502080.0    0.123    502080.0 ;   
> O02  C01  
> >    2   3   1    0.175    261918.4    0.175    261918.4 ;   
> C01  S01  
> >    3   4   1    0.133    313800.0    0.133    313800.0 ;   
> S01  HAA  
> >
> > [ pairs ]
> > ; ai  aj  fu    c0, c1, ...
> >    1   4   1                                           ;   
> O02  HAA  
> >
> > [ angles ]
> > ; ai  aj  ak  fu    c0, c1, ...
> >    1   2   3   1    120.0       418.4    120.0       418.4 ;   O02  
> > C01  S01  
> >    2   3   4   1     96.0       397.5     96.0       397.5 ;   C01  
> > S01  HAA
> >
> > [ dihedrals ]
> > ; ai  aj  ak  al  fu    c0, c1, m, ...
> >    1   2   3   4   1      0.0    2.9 3      0.0    2.9 3 ; 
> dih   O02  
> > C01  S01  HAA
> >
> >
> > put this file in ~/share/top  directory, run pdb2gmx to 
> convert this 
> > file to topology:
> >
> > HETATM    1  C01 C=O     1       0.000  -0.020   0.000  0.00  
> > 0.00           C
> > HETATM    2  S01 C=O     1       1.475  -0.886   0.000  0.00  
> > 0.00           S
> > HETATM    3  O02 C=O     1       0.000   1.188   0.000  0.00  
> > 0.00           O
> > HETATM    4  H01 C=O     1       1.860  -1.113  -1.263  0.00  
> > 0.00           H
> > HETATM    5  H03 C=O     1      -0.960  -0.584   0.000  0.00  
> > 0.00           H
> > CONECT    1    2
> > CONECT    1    3
> > CONECT    1    3
> > CONECT    1    5
> > CONECT    2    1    4
> > CONECT    3    1
> > CONECT    3    1
> > CONECT    4    2
> > CONECT    5    1
> > END
> >
> > and I have got this output:
> >
> > Select the Force Field:
> >  0: GROMOS96 43a1 Forcefield (official distribution)
> >  1: GROMOS96 43b1 Vacuum Forcefield (official distribution)
> >  2: GROMOS96 43a2 Forcefield (development) (improved alkane 
> dihedrals)
> >  3: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
> >  4: Gromacs Forcefield (see manual)
> >  5: gmx Forcefield with hydrogens for NMR stuff (Do NOT use 
> for new runs)
> > 0
> > Looking whether force field file ffG43a1.rtp exists
> > Opening library file /usr/local/gromacs/share/top/ffG43a1.rtp
> > Opening library file /usr/local/gromacs/share/top/aminoacids.dat
> > Reading drgnoh.pdb...
> > Read 3 atoms
> > Opening library file /usr/local/gromacs/share/top/xlateat.dat
> > 23 out of 23 lines of xlateat.dat converted succesfully
> > Analyzing pdb file
> > There are 1 chains and 0 blocks of water and 1 residues with 3 atoms
> >
> >   chain  #res #atoms
> >   1 ' '     1      3 
> >
> > All occupancies are one
> > Opening library file /usr/local/gromacs/share/top/ffG43a1.atp
> > Atomtype 50
> > Reading residue database... (ffG43a1)
> > Opening library file /usr/local/gromacs/share/top/ffG43a1.rtp
> > Residue 96
> > Sorting it all out...
> > Opening library file /usr/local/gromacs/share/top/ffG43a1.hdb
> > Opening library file /usr/local/gromacs/share/top/ffG43a1-n.tdb
> > Opening library file /usr/local/gromacs/share/top/ffG43a1-c.tdb
> >
> > Back Off! I just backed up topol.top to ./#topol.top.14#
> > Processing chain 1 (3 atoms, 1 residues)
> > Opening library file /usr/local/gromacs/share/top/specbond.dat
> > 5 out of 5 lines of specbond.dat converted succesfully
> > There are 0 donors and 0 acceptors
> > There are 0 hydrogen bonds
> > Fatal error: Residue 'C=O' not found in residue topology database
> >
> >
> > what is wrong? how can I generate a topology for this molecule?
> >
> >
> > __________________________________________________
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> >
> > 
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