[gmx-users] Ligand & Receptor

Justin A. Lemkul jalemkul at vt.edu
Fri Jun 26 15:32:48 CEST 2009

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:


Ignoring, of course, the parts about using PRODRG, but following pretty much 
everything else.


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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


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