Hi all,
For the GROMOS force field there's also the automated topology builder
(ATB) from Alpesh Malde and Alan Mark:
http://compbio.biosci.uq.edu.au/atb/
Cheers,
René
=====================================================
René Pool
Division of Molecular and Computational Toxicology
Department of Chemistry and Pharmaceutical Sciences
Vrije Universiteit Amsterdam
De Boelelaan 1083
1081HV AMSTERDAM, the Netherlands
-----
IBIVU/Bioinformatics
Department of Computer Science
Vrije Universiteit Amsterdam
De Boelelaan 1081a
1081HV AMSTERDAM, the Netherlands
Room P 2.75
E: r.p...@vu.nl
T: +31 20 598 76 12
F: +31 20 598 76 10
=====================================================
On 07/31/2011 05:21 PM, Andrej Frolov wrote:
Hello,
There are several ways to get the topology + force field for an
arbitrary molecule:
1. "Maestro + Desmond" programs of the Schrodinger software pack can
assign OPLS-AA force filed. The parameters are stored in the *.cms file.
2. "FFLD_SERVER" of the Schrodinger software:
$SCHRODINGER/utilities/ffld_server. Also OPLS-AA force filed.
You will need to write a script which converts the output to
Gromacs format.
3. "antechamber" + "tleap" of the AmberTools utilities. It can assign
any kind of Amber force field, like General Amber Force Field.
See an example:http://compchemmpi.wikispaces.com/Scripts#GenAmberTop
You could use the "amb2gmx" script to convert the generated Amber
topology to Gromacs format:
http://ffamber.cnsm.csulb.edu/ffamber-tools.html
4. ''PRODRG server'' for the united atom GMX force fields.
5. ''Vega ZZ'' and "Vega" can assign OPLS-AA force field, but not all
atom types, bonds etc. are supported.
6. "MCCCS Towhee'' monte carlo code can assign very many force
fields, but, first, one has to create the so-called basic connectivity
map (which atom is covalently bound to which).
http://towhee.sourceforge.net/
Kind regards,
Andrey
--
Andrey Frolov
PhD student
Max Planck Institute for Mathematics in the Sciences
(MPI f. Mathematik in den Naturwissenschaften)
Inselstr. 22-26, 04103 Leipzig, Germany
e-mail: fro...@mis.mpg.de
web: http://www.mis.mpg.de/scicomp/CompPhysChem/GroupMain.html
Dear all,
Is there any other free tool like PRODRG ? PRODRG server couldn't read
PDB file from user any more. It 's not easy to get a free version asap.
Best
Shiyong
--
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
