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

Hermann, Johannes J.Hermann at lrz.tu-muenchen.de
Tue Jul 4 08:25:14 CEST 2017

Hi Mark,

thank you for the hint with the scripts - I will try that!

So just to clarify: There is no way to manually consistently manipulate 
the .gro/.pdb and .top afterwards in order to e.g. change the 
protonation state (in an easy way)?

Thank you in advance!


On 03.07.2017 19:02, Mark Abraham wrote:
> Hi,
> 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."
> Mark
>> Thank you very much in advance!
>> All the best
>> Johannes
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*Technische Universität München*
*Johannes Hermann, M.Sc.*
Lehrstuhl für Bioverfahrenstechnik
Boltzmannstr. 15
D-85748 Garching
Tel: +49 8928915730
Fax: +49 8928915714

Email: j.hermann at lrz.tum.de

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