[gmx-users] Converting protonated protein with pdb2gmx

Deniz KARASU karasudeniz at gmail.com
Fri Oct 29 21:02:16 CEST 2010

Hi all,

I'm trying to convert a protein, that is protonated with another special
software and by manually checking,  with pdb2gmx. I am  using FF53A6
forcefield and don't use -ignh option. When I run pdb2gmx it gives me this

Atom HA in residue VAL 1 not found in rtp entry with 8 atoms
             while sorting atoms. Maybe different protonation state.
             Remove this hydrogen or choose a different protonation state.
             Option -ignh will ignore all hydrogens in the input.

I understand that the hydrogen atom is not defined in forcefield for VAL
residue and need selection protonation state interactively.

I wonder that there  is anyway to convert protonated protein for specified
forcefield (including united-atom ff) and assign automatically protonation
state according to bonded hydrogen in structure?


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101029/6b55a2d3/attachment.html>

More information about the gromacs.org_gmx-users mailing list