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.
Thanking you,
Cheers.
Soni Mufaddal Saifee,
B.Tech IIT Madras.
---------------------------------
Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now._______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
