[gmx-users] adding hydrogens to protein with pdb2gmx

Justin Lemkul jalemkul at vt.edu
Tue Sep 4 18:03:49 CEST 2012

On 9/4/12 11:59 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
> Yes okey. I understood.
> But I have another question:
> Since I only want to minimize the phosphates which I added to the protein
> I want to use the freeze option to make sure that the other residues will
> not change.
> But how can I say gromacs that it shell make an exception and do not
> freeze the phosphate of the residues where I added the phosphate?

Use the freezegrps option in the .mdp file, along with suitable index groups.


> Thank you,
> Eva
>> Only the -ignh flag is wrong, as Justin said.
>> Keep the rest of the command line.
>> --
>> Marcelo Depólo
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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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