[gmx-users] How to remove H atom from residue in gro file?

Justin A. Lemkul jalemkul at vt.edu
Thu Jan 17 19:37:32 CET 2008

Quoting Nelson Cotrim <nhcotrim at gmail.com>:

> Hi gmx users,
> I am rather new to MD, Linux environment and almost everything related
> to it. I am a geneticist working on mutations, so please, keep it
> simple :)
> This may be trivial and there may be an answer on the list already,
> but I do not even know how to search for it - the way I tried did not
> return anything useful.


Make sure the 'Mailing List' box is checked.

> I am analysing a mutation in a binding domain of a protein, and the
> ligand is phosporylated (a SER). I tried to use ff43a1p but kept
> getting errors in the FF files (hdb, rtp, etc), so instead I am used
> PRODRG to parametrize the PO4 (PO3+OG), changed the SEP to SER in the
> PDB file and then edited the .gro and .top files adding the data for
> the PO3.

Using the beta version of PRODRG, I hope?  The original server uses ffgmx, which
is a different force field.  Also note that the charges assigned by PRODRG are
often unsatisfactory.

> Evertyhting works great know, with the exception of the HG that
> pdb2gmx adds when converting the .pdb into the .gro. This HG is in the
> place that should be taken by the PO3, but I do not know how to remove
> it. Which values will I have to correct in the .top, if any? Should I

Well, if your residue is named SER, the .rtp file used by your force field will
try to assign all the atoms to a standard serine residue.  Then it will add
hydrogen atoms according to the corresponding entry in the .hdb file.

Having never used ffG43a1p, I can't provide a whole lot more input, but I would
also advise against removing parameters from your .top ad hoc.  You need to get
to the source of the problem instead of trying to create a solution.  What went
wrong with ffG43a1p in the first place?  Try searching using the above link, as
I know others have had issues with that particular force field.


> just remove the line with all the parameters and just correct the
> subsequent atom numbers? Is there an easier and foolpŕoof method to do
> this (it is easy to mistype the numbers this way)?
> Many thanks,
> Nelson
> --
> Instituto de Bioquímica Médica
> Universidade Federal do Rio de Janeiro
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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