[gmx-users] (Not-) Changing protonation when using pdb2gmx

Mark Abraham mark.j.abraham at gmail.com
Mon Jul 3 19:02:35 CEST 2017


You can use gmx pdb2gmx -lys interactively, or in a script with
http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts, but
you somehow have to know the order of the choices you want to make.

On Mon, Jul 3, 2017 at 6:50 PM Hermann, Johannes <
J.Hermann at lrz.tu-muenchen.de> wrote:

> Dear All,
> I am using pdb2gmx with the -lys flag in order to not protonate specific
> lysines. I have to do this for quit a few cases, where in most cases the
> lysines are protonated (as default in pdb2gmx).
> Is there a way to specify only the few cases, where I actually do not
> want to protonate (e.g. with residue id and/or chain)?
> Or can I manually delete the HZ3 LYS line after applying gmx2pdb with
> the default parameters and tell gromacs in the following commands not to
> touch the H atoms any more and leave the protonation state as it is?
> E.g. can I tell pdb2gmx not to change the protonation state of all
> residues and especially of the modified LYS when I rerun pdb2gmx for
> reordering the atoms (because I deleted one)?

Unfortunately there's no way to say e.g. "leave lysine the way it is."


> Thank you very much in advance!
> All the best
> Johannes
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