[gmx-users] Coordinate file does not match topology

Sheyore Omovie omovie_johnnie at hotmail.com
Tue Jun 12 19:17:37 CEST 2007

Thanks guys,
I've finally resolved it.
I think gromacs has an issue with the naming convention used in the pdb file 
I created with pymol.
So I started all over again, stripped the pdb file of its H-atoms. That way, 
both pdb2gmx and grompp worked just fine. pdb2gmx added the H-atoms I need 
in the structure.

>From: Yang Ye <leafyoung at yahoo.com>
>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] Coordinate file does not match topology
>Date: Mon, 11 Jun 2007 10:17:49 +0800
>On 6/11/2007 4:27 AM, David van der Spoel wrote:
>>Sheyore Omovie wrote:
>>>Thanks Yang,
>>>Each of the residues in my *.gro have more H-atoms than in *.top. I added 
>>>the 21 H-atoms in [molecules] section of *.top. But grompp still came up 
>>>with the ff error: No such molecule type.
>>>Do i have to edit [moleculetype] section too?
>>Please do not edit the topology file unless you are very sure what you are 
>>doing. You probably select a united atom force field and want to combine 
>>it with an all atom coordinate file. You will have to use the conf.gro 
>>that pdb2gmx produces.
>Hi, Omovie
>Hope David's comment help you to understand what you are doing with the 
>step of grompp. No individual H-atom shall exist outside a molecule as we 
>are not doing nuclear simulation. =)
>Yang Ye
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