[gmx-users] errors while runnning x2top command

[Rahul Karyappa]

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?

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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