[gmx-users] pdb2gmx error "residue not found in residue topology database"

[Peter Stern]

I never did that.


-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of su
Sent: Wednesday, July 08, 2015 11:26 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] pdb2gmx error "residue not found in residue topology database"

How you converted the gaussian file into .pdb? Because once i did the same and suffered from some missing co ordinates. 

Sent from my iPhone

> On 08-Jul-2015, at 11:16 pm, Peter Stern <peter.stern at weizmann.ac.il> wrote:
> 
> Look at the file: residuetypes.dat in the ../top/ directory of your installation.
> It lists all the residue names and more.
> 
> Peter Stern
> Weizmann Institute
> 
> Sent from my iPad
> 
>> On 8 ביולי 2015, at 17:45, Hamisu Aliyu Mohd <hamisu.kazaure at yahoo.com> wrote:
>> 
>> 
>> Dear gmx-users,
>> 
>> I am really new in this field of endeavour and I am trying investigate the solubility of peptides in organic solvents, I built a simple tripeptide (gly-gly-gly) using Gaussian 5.0 and I convert the output file(.out) to .pdb. I am now trying to use pdb2gmx tool to generate topology for my peptide using GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) I was promoted with an error "residue not found in residue topology database” I checked  GROMACS website at http://www.gromacs.org/Documentation/Errors I learned the residue must have the same name as in the force field, please I don’t know the naming convention of this force field please HELP.
>> 
>> Thanks 
>> Ali H.
>> Department of Chemistry
>> University Dutse
>> 
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