Thanks a lot for the quick response
Arik
On 2/26/2010 3:54 AM, Justin A. Lemkul wrote:
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:
http://chemistry.csulb.edu/ffamber/#install
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.
-Justin
Thanks a lot
Arik
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