[gmx-users] Renumber atom ids and charge group in topology (.itp)

Justin Lemkul jalemkul at vt.edu
Tue Dec 16 16:01:02 CET 2014

On 12/16/14 9:54 AM, Nash, Anthony wrote:
> Dear gromacs users,
> Renumbering the atom ids in a .gro file is very straight forwards, however, after cutting out the first 1/2 of my protein I am having great difficulty aligning my .itp file upon running grompp. Till this stage, it has been far easier for me to remove one particular domain of my protein from my pre-existing .gro file than it would be to adjusting the original crystal structure .pdb file and go through the great pains of getting pdb2gmx to work. But unfortunately I am now left with the fatal error:
> Atoms in the .top are not numbered consecutively from 1 (rather, atomnr = 2720, while at->nr = 0)
> which is quite understandable.
> I discovered an .awk file on the gromacs website. It is approx 5 years old and fails to renumber my atoms in the .itp file correctly. It fails at [ angles ]. I've been 'googling' for a solution but I am yet to find one.

If you're hacking off part of the protein, the most straightforward solution is 
to just regenerate a new topology with pdb2gmx.


> All help is appreciated.
> Thanks
> Anthony
> Dr Anthony Nash
> Department of Chemistry
> University College London


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