Chris
This is, what I usually do, too.
Still you need the parameters for your ligand from somewhere ;)
Regards
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.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.
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
.
_______________________________________________
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
