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

Nelson Cotrim nhcotrim at gmail.com
Thu Jan 17 18:20:40 CET 2008

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,

Instituto de Bioquímica Médica
Universidade Federal do Rio de Janeiro
Av. Bauhinia 400 CCS, Bl. E, sl 22
Ilha do Fundão - Rio de Janeiro - RJ
Tel: 55-21-2562-6759
Cel: 55-21-9267-3067

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