[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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> >
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