[gmx-users] State B IN Topology
jalemkul at vt.edu
Wed Feb 24 15:49:23 CET 2016
On 2/23/16 7:18 PM, Sana Saeed wrote:
> HIi am making topology of protein ligand complex for calculating binding free
> energy. my question is do i need to define state B manually or is there any
> automatic method to do that. Second question is i want of number my ligand
If it's an absolute binding free energy, everything is handled in the .mdp file
via couple-moltype and options related to the lambda vector. If it's a relative
binding free energy, you must manually specify the B-state in the topology.
> atom numbers from the number where protein atom numbers are stopped , like if
> protein's last atom is 100 then i want to start my ligand from 101. manually
> it will take lots of time because i will have to modify all the sections in
> topology file, is there any easy method? or i need to do that manually.
You should not do this. You don't need to, and even if you do it, grompp will
fail because the [moleculetype] will not be numbered from 1. The global atom
numbers in the coordinate file have no bearing on the [moleculetype] numbering
in the topology. The atoms need to be in the same order. There is no need to
merge topologies to carry out free energy calculations.
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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