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

[Hamisu Aliyu Mohd]

Thank You Mr. Peter I just checked your response and that really helps.
Gaussian allows you to save the file in different format(.pdb inclusive), I just choosed to save in .pdb format. I don’t know if I did the right thing. hahaha...
On Jul 9, 2015, at 8:17 PM, su <sun.iba2 at gmail.com> wrote:

> Peter, This question was for Ali.H.. 😉
> 
> Sent from my iPhone
> 
>> On 09-Jul-2015, at 5:20 pm, Peter Stern <peter.stern at weizmann.ac.il> wrote:
>> 
>> 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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