Jack Shultz wrote:
Hello,
I'm trying to figure out how I can merge the ligand and receptor
files. I used this script to prep a ligand I treated with GAFF
perl amb2gmx.pl --prmtop test1.prmtop --crd test1.inpcrd --outname ligand
This results in ligand.top & ligand.gro
Then I prepped a receptor
pdb2gmx_d -f fzd2.pdb -ff amber03 -o conf.pdb
Is there some way to merge these structures and then simulate with gromacs?
Well, you will have to choose one format - either .pdb or .gro - for both ligand
and receptor, then you could conceivably merge those two files. Probably it's
best if you follow the drug-enzyme tutorial here:
http://oldwiki.gromacs.org/index.php/Tutorials
Ignoring, of course, the parts about using PRODRG, but following pretty much
everything else.
-Justin
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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