- 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
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