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

Nash, Anthony a.nash at ucl.ac.uk
Tue Dec 16 15:54:05 CET 2014

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.

All help is appreciated.

Dr Anthony Nash
Department of Chemistry
University College London

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