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.
Cheers,
Michel
On 10/12/2010 02:28 PM, gmx-users-requ...@gromacs.org wrote:
Part 1.2
Subject:
Re: [gmx-users] Re: swiss param query
From:
David van der Spoel <sp...@xray.bmc.uu.se>
Date:
Tue, 12 Oct 2010 19:27:26 +0200
To:
Discussion list for GROMACS users <gmx-users@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
Switzerland
http://lausanne.isb-sib.ch/~mcuendet/
==========================================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
