[gmx-users] Generating topology file for a molecule (FNP) not in the gromacs library.
mgoette at mpi-bpc.mpg.de
Fri Jan 11 11:23:44 CET 2008
This is, what I usually do, too.
Still you need the parameters for your ligand from somewhere ;)
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
Chris Neale wrote:
> When actually building the topology I find it easiest to create the
> residues in the relevant .rtp and allow pdb2gmx to build the topology
> for you. However, all this does is correctly connect everything and put
> your parameters where they should be. All previous comments (in this
> thread and the hundreds of other threads on this topic) still apply
> about how to come up with the parameters... read the original papers and
> reproduce their methodology.
>> Dear users,
>> I am working with PTP1B protein. Recently I tried to
>> run it in gromacs along with an inhibitor
>> 2-YL]-DIFLUORO-METHYL}-PHOSPHONIC ACID [FNP in short]. The problem
>> is that gromacs does not recognize FNP and hence I am not able to
>> generate a topology file of it using pdb2gmx. I tried using the The
>> Dundee PRODRG server to generate the topology file with the pdb file
>> as the input. The problem is that it does generate the topology file
>> but without any hydrogens. Even the polar hydrogens information is
>> not available inspite of it being a part of my input pdb file. Thus I
>> am not able to use FNP with the polar hydrogens for my runs.
>> If anyone has faced similar problems please do help if you can.
>> Thanking you,
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