[gmx-users] fatal error [using pdb2gmx]

Sven Huttenhouse mdsimulation at hotmail.com
Tue Oct 18 19:36:02 CEST 2005

Many thanks Dr. Erik for your help.
I still have some doubts about atoms naming. in the file ffG43a1.rtp I find 
CA sometimes represent  a carbon in a CH2 group and sometimes a carbon in a 
CH ??
Sometimes find numbers used to distinguish between atom from the same type 
and sometimes letters, like HA1 HA2 or O1 O2 O3 and sometimes CA CB CD 
representing carbon in a CH2 group??
Is there any source where I can find the explanation of atoms naming?
Also I'm trying to find a source that explains the pdb file format.
I will really appreciate it is someone can guide me in how to construct a 
pdb file for any molecule like if I want to write my own pdb file for 
Many thanks
Sven Huttenhouse

>From: Erik Lindahl <lindahl at sbc.su.se>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] fatal error [using pdb2gmx]
>Date: Mon, 17 Oct 2005 17:46:43 +0200
>Hi Sven,
>The problem with the glycine in the latter place is that the atom  
>names/enumeration are wrong.
>Gromacs relies on the standard PDB names, and then optionally adds  the 
>termini itself.
>You can find the correct/expected atom names for each force field in  the 
>ffNAME.rtp file, e.g. ffoplsaa.rtp (in the share/top dir).
>If there are problems with the termini you can just remove the extra  atoms 
>and let Gromacs recreate them for you. I've attached a proper  GLY.pdb file 
>with hydrogens. If you are using a united-atom force  field (e.g. Gromos96) 
>you need to use the -ignh option to pdb2gmx,  though.

><< gly.pdb >>

>Erik Lindahl  <lindahl at sbc.su.se>
>Assistant Professor, Stockholm Bioinformatics Center
>Stockholm University, SE 106 91 Stockholm
>Phone: +46 8 5537 8564     Fax: +46 8 5537 8214

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