[gmx-users] fatal error [using pdb2gmx]

Sven Huttenhouse mdsimulation at hotmail.com
Mon Oct 24 20:05:21 CEST 2005

Thank you Dr. Erik for your help.

I've used the glycine pdb file that you sent to me and I was able to 
generate a (.gro) and a (.top) files using pdb2gmx.
I was also able to riplicate it and generate 200 molecules in a pdb file 
(200glyc.pdb) using genbox.
howevar, when I tried to generate a (.gro) file from the (200glyc.pdb) file 
using pdb2gmx I got the following error message:

Fatal error: Atom H1 in risidue GLY 2 not found in rtp entry with 7 atoms 
while sorting atoms. maybe different protonation state. remove this hydrogen 
or choose a different protonation state. Option -ignh will ignore all 
hydrogens in the input.

I used force field # 3. Could you please explain to me how can I solve this?

kind regards

>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: Tue, 18 Oct 2005 20:13:28 +0200
>On Oct 18, 2005, at 7:36 PM, Sven Huttenhouse wrote:
>>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 
>That would be IUPAC (International union of pure and applied  chemistry). 
>Since the ASCII character set doesn't contain greek  glyphs we use CA=alpha 
>carbon, CB=beta carbon, CG=gamma carbon,  CD=delta carbon, etc.
>Please not that there are two different concepts:
>1. The name of an individual ATOM. Each atom in a molecule should  have a 
>unique name.
>2. The name of the atomtype in the forcefield used.
>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
>gmx-users mailing list
>gmx-users at gromacs.org
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