[gmx-users] Atomtype OW not found

[Tamir Dingjan]

Hi Rasha,

I suspect your difficulties might be caused by the way you are converting
the parameters. You may have more luck using acpype
<https://code.google.com/p/acpype/> to convert your GLYCAM carbohydrate
topologies into Gromacs formatted ones. Once you obtain your ligand
coordinate and parameter files (either from the GLYCAM website or through
AMBER), run acpype to convert the files into Gromacs formats - here's the
command I use: acpype.py -x 1.rst7 -p 1.parm7 -o gmx

If you are using the AMBER force field in Gromacs for simulation, this
method will be compatible with the usual water models.

Regards,
Tamir

On 4 June 2015 at 00:33, Barnett, James W <jbarnet4 at tulane.edu> wrote:

> What does your topology (.top) file look like? And what's the exact
> command you are using for grompp?
>
> --
> James “Wes”​ Barnett
> Ph.D. Candidate
> Chemical and Biomolecular Engineering
>
> Tulane University
> Boggs Center for Energy and Biotechnology, Room 341-B
> New Orleans, Louisiana 70118
> jbarnet4 at tulane.edu​
> LinkedIn​​
>
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Rasha
> Alqus <rasha.alqus at manchester.ac.uk>
> Sent: Wednesday, June 3, 2015 8:39 AM
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Atomtype OW not found
>
> Dear Gromacs users,
> I am trying to run an md of carbohydrate systems in water, the pdb of
> carbohydrate produced in glycame builder, files were loaded in amber to
> produce topolgy file and coordinate using glycame force file.
> I have run glycam2gmx.pl script to convert files into gromacs ones. I
> would like to solavte the sytem using tip5p, but when i run the grompp i
> get an error
>
> program grompp_d, VERSION 4.5.4
> Source code file: toppush.c, line: 1166
> Fatal error:
> Atomtype OW not found
> For more information and tips for troubleshooting, please check the GROMACS
>
> I also tried to do that with other water model and it give me the same
> issue, can you please help me to solve that issue.
>
> Thank for the help
> Regards
> rasha
>
>
>
>
>
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-- 

*Tamir Y. Dingjan*

*B. Pharm Sci (Hons), MRACI*

*PhD Candidate  <http://www.linkedin.com/pub/tamir-dingjan/50/282/82b>*


Medicinal Chemistry

*Monash Institute of Pharmaceutical Sciences,*

*Monash University*
381 Royal Parade

Parkville, Victoria 3052, Australia



p: + 61 3 9903 9187

e: tamir.dingjan at monash.edu