[gmx-users] (Not-) Changing protonation when using pdb2gmx
J.Hermann at lrz.tu-muenchen.de
Mon Jul 3 18:49:54 CEST 2017
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)?
Thank you very much in advance!
All the best
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