[gmx-users] pdb2gmx and arginine

Yang Ye leafyoung at yahoo.com
Tue Jun 19 13:10:55 CEST 2007

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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