[gmx-users] protonation state

David spoel at xray.bmc.uu.se
Sat Nov 9 11:52:36 CET 2002

On Sat, 2002-11-09 at 04:11, Wei Fu wrote:
> Hi, all,
>      When I consider the protonation state on dopamine receptor I found that in "pdb2gmx -inter" there is no option for ARG residue, why so? I think ARG is also an improtant residue for protonation state and I would like to consider its protonation state, how do I consider it?  Or am I wrong?
>      Thanks for any reply in advance!
doesn't it have very high pKa?
Otherwise, it's not so complicated, you need new charges and to verify
the Lennard Jones parameters. It obviously depends as well on which
proton is taken off.
>www interface or send it to gmx-users-request at gromacs.org.
Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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