[gmx-users] pdb2gmx and arginine

Roberto Marchese roberto.marchese at gmail.com
Tue Jun 19 11:29:05 CEST 2007

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?

I have found at this link
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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