[gmx-users] how to convert CGenFF into .itp file?
David van der Spoel
spoel at xray.bmc.uu.se
Wed Dec 26 19:53:38 CET 2012
On 2012-12-26 13:00, Albert wrote:
> On 12/26/2012 12:39 PM, Peter C. Lai wrote:
>> It should come with two files. A .prm file, which contains the actual
>> forcefield parameters that you use the script to convert to bonded and
>> nonbonded .itp and atomtypes.atp The .rtf file is the charmm
>> equivalent of
>> our .rtp file: it contains some premade residue topologies with charge
>> connectivity information. I don't know if there are scripts to convert
>> this or
>> not, but it's easy enough to get what you need by hand especially
>> since if
>> your ligand isn't in there, you'll have to create the .rtp entry on
>> your own
>> or get them from paramchem anyway...
> THX for comments. It works now and I get a folder called cgenff-2b7.ff
> like what we seen in the share/top folder for other FF.
> that's too complicated to real use. Initially, I thought that the
> output for the ligand should be a single .itp file like what we found in
> Probably one can consider improve this script. As far as I know the
> CGenFF website can export full parameters for the ligand even it is
> already exist in CGenFF off line files. In this cases, the output file
> fro CGenFF website is independent from the offline FF and it already has
> complete necessary information for paramters and topology). Probably one
> can consider improve this script and export the output file as a single
> .itp file.
Hey, it's open source. Let us know how it goes :).
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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