Yang Ye wrote:
On 6/19/2007 5:29 PM, Roberto Marchese wrote:
Dear GROMACS Users,
the OPLSAA force field (implemented in gromacs), have a notation for
deprotonated arginine ARGN vs ARG (charge 0). The utility pdb2gmx
don't give do possibility to set arginine protonation state, like LYS,
HIS ...
There are a way to overcome this problem?
Replace ARG with ARGN in your PDB or GRO file.
it won't work out of the box, see
http://bugzilla.gromacs.org/show_bug.cgi?id=97
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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