[gmx-users] Amber and protonation state

Justin A. Lemkul jalemkul at vt.edu
Fri Feb 26 12:54:43 CET 2010

Arik Cohen wrote:
> Dear users,
> I would be most thankful for any comment or advice on the following 
> problems:
> 1. I'm running GROMACS 4.04 with amber V_4.0. /amber99sb forcefield. 
> While executing the pdb2gmx command as: pdb2gmx -f 1bgq.pdb -water tip3p 
> -his
> the -his option does not work regardless of the choice in the 
> protonation state
> 2. Is there any way to change the protonation state not via an 
> interacticve mode and thus to enable to run the pdb2gmx in an automatic 
> way(echo 10 | pdb2gmx ... | -his echo 2 will not work of course)

Point #10 in the ffamber "Installation and Testing" section:


You can solve all protonation issues by having the right residue names to start. 
  The Gromacs conventions for, e.g. histidine, are HISA, HISB, and HISH.  For 
Amber, the corresponding residue names are HID, HIE, and HIP.  If you go through 
your .pdb file and re-name residues in advance, the proper protonation states 
will be assigned.  This also applies to any other titratable residues, and 
termini, which must be prefixed with N and C.


> Thanks a lot
> Arik


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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