[gmx-users] one protein and 4 ligands

Justin Lemkul jalemkul at vt.edu
Mon Dec 4 15:28:00 CET 2017

On 12/3/17 11:27 PM, Mahboobeh Eslami wrote:
> Dear justinThank you so muchI did MD simulation on some protein-ligand complexes but I don't know that I must use one mol2 file for 4 ligands or  separate mol2 files for each ligand. I want to calculate free energy value for this complex by GMXPBSA script. Must free energy value be calculated for 4 lignads simultaneously? or I can calculate free energy value for each lignad individually.Thank you for kindness

No idea. How do people deal with such a situation in the literature?



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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