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.
Chris.
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.
_______________________________________________
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
