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

Nash, Anthony a.nash at ucl.ac.uk
Tue Dec 16 16:16:56 CET 2014

Hi Justin,

If there isn't there isn't. I was just hoping to save myself the effort of correcting for the missing atoms on the crystal structure and the conversion of HIS to HIE/HID with the amber forcefield. 


Dr Anthony Nash
Department of Chemistry
University College London
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Justin Lemkul [jalemkul at vt.edu]
Sent: 16 December 2014 15:00
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Renumber atom ids and charge group in topology (.itp)

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

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