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

Maik Goette mgoette at mpi-bpc.mpg.de
Fri Jan 18 09:42:57 CET 2008


First of all, I think its dangerous to perform MD simulations without 
any knowledge about the details of MD.
So the first suggestion is: Inform yourself (by reading the manual) 
about MD and GROMACS. Using a black box is, maybe, often done, but 
surely not the best way to go.
Before starting a simulation with non-standard residues I'd suggest to 
start some tutorial-simulations with "normal" proteins to improve your 

To solve your problem the easiest (and hopefully the best) way, I would 
suggest to use the amberFF port and then build your phosphorylated 
residues according to these parameters:
N Homeyer, AHC Horn, H Lanig, H Sticht - Journal of Molecular Modeling, 2006

This is for sure some work and you need an understanding of how GROMACS 
makes use of residue parameters and stuff, but its IMHO the best way to 
produce reasonable results.


Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/

Nelson Cotrim wrote:
> 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.
> 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.
> 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
> 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
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