[gmx-users] pdb2gmx and arginine

[David van der Spoel]

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
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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