[gmx-developers] modify pdb2gmx and/or g_protonate in order to add specific hydrogen name
landry.charlier at univ-montp1.fr
Fri Feb 1 09:50:07 CET 2013
I have some problems in order to automatically add hydrogen to lipids
with charmm36 force field. Indeed, when several hydrogen have to be
added to the same atom, the command pdb2gmx -ignh or g_protonate add
them with the same name but with the last number incremented by 1
thanks to the .hdb file.
Example : for charmm36, the hydrogens added to the CB atom of ARG are
named HB1 & HB2 thanks to the line "2 6 HB CB CG CA" in the
For lipids, the hydrogen names differ by a letter. H13A, H13B H13C are
linked to C13 in POPC in charmm36 for example.
I would like to modify g_protonate or pdb2gmx in order to add hydrogen
with a specific name like that:
- If only 1 name is written in hdb file and several atoms have to be
added, the hydrogen names have been incremented by 1 as it's by
default (see the example of Arg above).
- If there are as many names as the number of hydrogen to add, pdb2gmx
and/or g_protonate will choose these names. The hdb file should be
like this : 3 4 H13A,H13B,H13C C13 N C12
But I check the g_protonate and pdb2gmx files in the source code and I
am not enough good in programming for modify them.
Could you help me please?
More information about the gromacs.org_gmx-developers