AMBER Archive (2008)

Subject: Re: AMBER: Regarding neutral Arginine unit

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Jan 15 2008 - 10:28:21 CST

I don't think so since arg pka is 12 or so. are you sure you want to
do this? it can really change your prot to neutralize the side chains.

On 1/15/08, jani sahil <genomejani_at_gmail.com> wrote:
> Hello ,
> I am simulating a acid protease which is charged protein.
> So I want to neutralize all the charged side chains. I can see
> that amber has parameters for neutral forms of Asp, Glu, Lys and His, but
> I don't see a neutral form for Arg
>
> please can any one suggest e how i can neutralize Arg
>
> Thanking in anticipation
>
>
> Regards
> Jani Vinod
> 

-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor                 Phone: (631) 632-1336
Center for Structural Biology       Fax:   (631) 632-1555
CMM Bldg, Room G80
Stony Brook University              E-mail: carlos.simmerling_at_gmail.com
Stony Brook, NY 11794-5115          Web: http://comp.chem.sunysb.edu
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