[gmx-users] adding hydrogens to protein with pdb2gmx
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,
>> Only the -ignh flag is wrong, as Justin said.
>> Keep the rest of the command line.
>> Marcelo Depólo
>> gmx-users mailing list gmx-users at gromacs.org
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> * Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users