Mufaddal Soni wrote:
Dear users,
I am working with PTP1B protein. Recently I tried to
run it in gromacs along with an inhibitor
{[7-(DIFLUORO-PHOSPHONO-METHYL)-NAPHTHALEN-
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.
Have you read
http://wiki.gromacs.org/index.php/Exotic_Species ?
Note however, that parametrizing some exotic molecule is a non-trivial
issue...
Good luck, Jochen
Thanking you,
Cheers.
Soni Mufaddal Saifee,
B.Tech IIT Madras.
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--
************************************************
Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
************************************************
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