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

Hermann, Johannes J.Hermann at lrz.tu-muenchen.de
Mon Jul 3 18:49:54 CEST 2017

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)?

Thank you very much in advance!

All the best


More information about the gromacs.org_gmx-users mailing list