[gmx-users] Re: swiss param query

Michel Cuendet michel.cuendet at isb-sib.ch
Tue Oct 12 23:10:07 CEST 2010

Hi David,

Yes indeed, there are multiple ways to get a mol2 files besides using 
chimera. You can get it from ZInc, or use openbabel or Marvin Sketch to 
generate it, for example.

The result normally comes back within minutes. Are you sure you included 
all hydrogens in the mol2 file? Sometimes the system detects a problem 
in your mol2 file, and the webpage following the submission tells you 
what happened. Maybe you didn't see that if you were trying to make the 
submission non-interactive.

We did not plan to have a non-interactive version of the server online 
for now. But if you need a series of molecules for a given project, we 
can certainly generate the topologies for you. Please get back to me 
regarding this.



On 10/12/2010 02:28 PM, gmx-users-request at gromacs.org wrote:
> Part 1.2
> Subject:
> Re: [gmx-users] Re: swiss param query
> From:
> David van der Spoel <spoel at xray.bmc.uu.se>
> Date:
> Tue, 12 Oct 2010 19:27:26 +0200
> To:
> Discussion list for GROMACS users <gmx-users at gromacs.org>
> By the way Michel,
> your website looks very interesting. I would like to make this process 
> non-interactive, and can generate a mol2 file from a pdb file using 
> babel (if the pdb file has H already of course) and hence skip the 
> chimera step. I just submitted a molecule but haven't got the result 
> yet, is there an off-line version? Or one where I can send 200 molecules?
Michel Cuendet, Ph.D
Molecular Modeling Group
Swiss Institute of Bioinformatics
CH-1015 Lausanne

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