----- Original Message ----- From: Jack Shultz <j...@drugdiscoveryathome.com> Date: Friday, January 29, 2010 4:15 Subject: [gmx-users] including a custom itp file in topology To: Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Alan <alanwil...@gmail.com>, Andrey Voronkov <a...@drugdiscoveryathome.com>
> Hi, > > I was trying to figure out if there is a short-cut for what I'm doing. I have > complexes that I'm trying to prep using pdb2gmx. The ligand does not have a > standard residue name. The way I know this can work is seperating out the > ligand and protein into seperate files and preping the ligand using acpypi > and the protein using pdb2gmx. Then incorporating them into a single pdb > complex and including a reference to the ligand.itp (generated by acpypi) > into a complex topology file. Is there any shortcut to doing this? any way to > reference the ligand's itp file when running pdb2gmx? The procedure looks good, but there's no way to get pdb2gmx to do this step for you. It will be straightforward to use sed or perl to add the #include and the [molecules] changes into the .top produced by pdb2gmx - that's what these tools are for! Even head -n -2 topol.top > new.top echo '#include "ligand.itp"' >> new.top tail -n 2 topol.top > footer >> new.top echo 'ligand 1' >> new.top will do the job if the last two lines of topol.top are of the form [molecules] Protein 1 This kind of UNIX-tool scripted problem-solving using head, tail, cut, paste, grep, sed, uniq, sort, echo, perl, cat and others often requires some consultation of the man pages and awareness that the tool exists... but most problems you want to solve have been solved before and the tool is out there already... Google away! Mark -- gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
