[gmx-users] Re: PRODRG tools

Andrej Frolov frolov at mis.mpg.de
Sun Jul 31 17:21:45 CEST 2011


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:
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).

Kind regards,
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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