[gmx-users] Re: PRODRG tools

[René Pool]

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.pool at 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: frolov at 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
>>
>
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