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.
I have found at this link
http://www.krugle.com/examples/p-2R7KSPYdeW4OI1tn/pdb2gmx.c
the source code of pdb2gm.c, this source implement the option '-arg',
for the definition of arginine protonation state, but the problem is
that the site state that this source is in the package released from
gromacs.org. I have downloaded the package, but the
pdb2gmx.c(gromcas/src/kernel/pdb2gmx.c) is different, it don't have
the arginine manager code.
Do Someone have some explanation?
Thanks To All
Roberto Marchese
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