[AMBER] ligand force field

From: hosein geraili <geraili_hosein.yahoo.com>
Date: Fri, 2 Nov 2018 18:22:13 +0000 (UTC)

I used force field parameters from an article for a ligand inside a protein, so I created the ligand.lib and ligand.frcmod files, now I wanna use these files along with the main pdb file of the protein which has the ligand inside, and load this pdb, ligand.lib, and ligand.frcmod in tleap to get the .prmtop and .inpcrd for all the atoms, but the problem is if I retain the ligand atoms inside the pdb file in the final .inpcrd and .prmtop there will be two ligand, and if I delete all the ligand atoms from the pdb file, there will be no ligand in the final .prmtop and .inpcrd.Any comment on that??Best
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Received on Fri Nov 02 2018 - 11:30:02 PDT
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