AMBER Archive (2004)

Subject: Re: AMBER: CAP PROTOCOL SIMULATION

From: Oliver Hucke (ohucke_at_u.washington.edu)
Date: Tue May 18 2004 - 16:07:45 CDT

Ray and Andreas,

may I ask which version of sander you use for "cap simulations"?
I would also be interested in the value of "cut".

I am asking because I did get reasonable results with a cap and sander8
only with an infinite cutoff, which made the calculations very slow...

Thanks very much,
Oliver

Ray Luo wrote:
> Andreas Svrcek-Seiler wrote:
>
>> Hi,
>>
>>> Could anybody tell me a good reference or an idea for a protocol to deal
>>> with caps of water and Poisson-Boltzmann ?
>>> My basic cuestion is how should I minimize the solvated complex before
>>> molecular dynamics.
>>> Is it better to freeze solute and minimize water separately or should I
>>> directly minimize the entire complex?
>>>
>>

........

______________________________________________________________

Oliver Hucke, Dr.
                               Health Sciences Building - K418C
University of Washington 1959 NE Pacific St.
Dept. of Biochemistry phone: (206) 685 7046
Box 357742 fax : (206) 685 7002
Seattle, WA 98195-7742 email: ohucke_at_u.washington.edu
_______________________________________________________________

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