[gmx-users] Residue renaming during mdrun

Justin Lemkul jalemkul at vt.edu
Mon May 13 13:51:01 CEST 2013

On 5/13/13 6:30 AM, Laura Leay wrote:
> All, I have a system of nitric acid modelled as NO3- and HO3+ plus SPC water. After setting the system up using genbox I then energy minimise. Althouth the input conf.gro file looks fine (NO3- labelled 'NO3', HO3+ labelled 'HO3' and water labelled 'SOL') the confout file has all of the H3O renamed to 'SOL'. This makes it difficult to analyse my system if I can't distinguish between water and hydronium.
> To construct the system I started with a single NO3- and a single HO3+ in separate gro files. I used the following commands in this order:
> genbox -cs NO3.gro -nmol 124 -box 4 4 4 -o NO3conf.gro
> genbox -cp NO3conf.gro -ci hydronium.gro -nmol 124 -o NO3+H3Oconf.gro
> genbox -cp NO3+HO3conf.gro -cs -o conf.gro
> This results in the following order in the gro file: NO3, HO3, SOL (I manually edit the topology file so that the number of water molecules matches those added by genbox).
> This is the same as the order in the topology file. Residues in the topology file have the same name as in the original gro files.
> I should point out that I'm using my own force field file, based on information on the literature, with the parameters for SPC water taken from the gromacs AMBER force field (all the literature data is based on AMBER). I don't see that this would affect residue naming though.
> I'm using gromacs v 4.5.4
> If anyone can shed some light on this, or suggest a work around, I'd appreciate it.

Residue naming in output files is dependent upon residue naming found in the 
topology.  If the coordinate file is out of order with respect to the topology, 
grompp warns about this very clearly.  Naming mismatches are the only way I can 
see that this would happen.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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