Hi,<br><br>Contrary to Chris, I think it's easier/better to leave the .rtp database for building blocks of chains (and definitely advocate against bothering with the file for newbies). Small ligand topologies are better made seperately "by hand" and inserted in manner similar to the procedure in John Kerrigan's tutorial.
<br>In any case, for compounds with names like {[7-(DIFLUORO-PHOSPHONO-METHYL)-NAPHTHALEN-2-YL]-DIFLUORO-METHYL}-PHOSPHONIC ACID, I would scratch my head a few times and probably go search for a different project. It's a charged fairly large, complex small molecule ;) with everything conjugated, which makes it a daunting task to derive proper parameters. For example, PRODRG will likely return you a naphtalene ring with no charges, quite contrary to what you would expect, and which may be necessary for the interaction with positive charges (a la cation-pi interaction).
<br><br>But these are just my two cEUR (which now is ~ 3 cUSD by the way ;))<br><br>Cheers,<br><br>Tsjerk<br><br><div class="gmail_quote">On Jan 10, 2008 7:34 PM, Chris Neale <<a href="mailto:chris.neale@utoronto.ca">chris.neale@utoronto.ca
</a>> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">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.
<br><br>Chris.<br><br>>Dear users,<br>> I am working with PTP1B protein. Recently I<br>>tried to run it in gromacs along with an inhibitor<br>>{[7-(DIFLUORO-PHOSPHONO-METHYL)-NAPHTHALEN-<br>>2-YL]-DIFLUORO-METHYL}-PHOSPHONIC ACID [FNP in short]. The
<br>>problem is that gromacs does not recognize FNP and hence I<br>>am not able to generate a topology file of it using pdb2gmx. I<br>>tried using the The Dundee PRODRG server to generate the<br>>topology file with the pdb file as the input. The problem is
<br>>that it does generate the topology file but without any<br>>hydrogens. Even the polar hydrogens information is not<br>>available inspite of it being a part of my input pdb file.<br>>Thus I am not able to use FNP with the polar hydrogens for my runs.
<br>><br>>If anyone has faced similar problems please do help if you can.<br>><br>>Thanking you,<br>>Cheers.<br><br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">
gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">
http://www.gromacs.org/search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org
</a>.<br>Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br></blockquote></div><br><br clear="all"><br>-- <br>Tsjerk A. Wassenaar,
Ph.D.<br>Junior UD (post-doc)<br>Biomolecular NMR, Bijvoet Center<br>Utrecht University<br>Padualaan 8 <br>3584 CH Utrecht<br>The Netherlands<br>P: +31-30-2539931 <br>F: +31-30-2537623