[gmx-users] State B IN Topology

Justin Lemkul 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


More information about the gromacs.org_gmx-users mailing list