[gmx-users] Ligand & Receptor

Jack Shultz js at drugdiscoveryathome.com
Fri Jun 26 15:26:53 CEST 2009


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?


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