[gmx-users] renumber ligand atom numbers

Justin Lemkul jalemkul at vt.edu
Sat Feb 27 13:14:16 CET 2016

On 2/27/16 6:04 AM, Sana Saeed wrote:
> hii am performing protein ligand binding free energy calculation through
> alchemical pathway. i made both topologies and generated distance, dihedral
> and angle restraints. in the index file i defined the restrained atoms. the
> error i got in energy minimization grompp is that the atom is out of range.
> it is because my protein is starting from atom num 1 and also my ligand
> starts with 1. in the gro file the numbering is changed , protein starts with

No, grompp is complaining because (I'm guessing, since you haven't provided us 
with an exact error message) you're specifying a completely nonexistent atom 
number somewhere.

> 1 and ends with 1020 , and ligand starts after 1020. but in topology i
> included the ligand.itp (from acpype) into complex topology file, and both
> molecules starts with 1. how can i change the numbering of ligand atoms as in

Don't alter the topology numbering.  It is a different concept from number in a 
coordinate file.  All [moleculetype] definitions MUST start from 1.  If you 
alter it, grompp will fail for a different reason.  Sort out the grompp problem 
you have now, not the one you'll create by breaking your topology.


> gro file. pdb2gmx -renum is not working because it is small ligand not a
> protein or peptide. if there is any code or any program please suggest.
> thanks in advance. Sana Saeed Khan,Teaching-Research
> AssistantChemoinformatics LabGraduate Student, MS bioinfoDepartment of
> BioinformaticsSoongsil University, Seoul, South Korea.


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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