[gmx-users] errors while runnning x2top command

[David van der Spoel]

Rahul Karyappa wrote:
> Actually Sir, my structure contains aluminium and silicon atoms which 
> PRODRG does not support. And using pdb2gmx I get lots of errors. So by 
> running x2top command I can get .top file. But for x2top errors which I 
> have mentioned, how can I proceed?

There is not much force field support for any of these atoms, only for 
silicium oxided like structures. You will have to copy the ffmgx.n2t 
file to your working directory and edit that to make a topology. Then 
you will have to get force field parameters from literature and add them 
in the appropriate force field files, e.g. ffgmxnb.itp



> Waiting for your kind reply.
> 
> Rahul Karyappa
> */-- Original Message --/*
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Date: Sat, 26 Nov 2005 14:14:49 +0100
> Subject: Re: [gmx-users] errors while runnning x2top command
> 
> 
> Rahul Karyappa wrote:
>  > Dear all,
>  > I wanted to generate the topology file using x2top command. When I
>  > gave the command:
>  > x2top -f conf.gro -o out.top -r out.rtp -param
> 
> x2top is really a last resort for special cases. Have you tried pdb2gmx
> (proteins) or the PRODRG server for small molecules?
> 
>  >
>  > it gave me following error:
>  > 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)
>  > 4
>  > Looking whether force field file ffgmx.rtp exists
>  > Opening library file /usr/local/gromacs/share/top/ffgmx.rtp
>  > Generating bonds from distances...
>  > Opening library file /usr/local/gromacs/share/top/ffgmx.atp
>  > There are 54 type to mass translations
>  > atom 615
>  > Opening library file /usr/local/gromacs/share/top/ffgmx.n2t
>  > There are 20 name to type translations
>  > Fatal error: No forcefield type for atom OA (4) with 4 bonds
>  >
>  > Where I need to make changes? Please help me out. I wanted to create a
>  > topology file. I started doing it manually but it is very time-consuming
>  > and also it is tedious job. Thanking you in advance.
>  >
>  > Rahul Karyappa
>  >
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> 
> -- 
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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