Re: [AMBER] question about bond command

From: Jason Swails <jason.swails.gmail.com>
Date: Sun, 25 Jul 2010 01:13:51 -0400

This is detailed quite thoroughly in the manual. I would also suggest reading the original implementation article by Mongan et al. The full citation is in the amber manual. This paper does a good job of telling you exactly what is done for constant pH MD in amber.

All the best,
Jason

--
Jason Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
On Jul 24, 2010, at 12:34 PM, Philippe Pinard <pp_amber17.yahoo.com> wrote:
> Thanks a lot. Very helpful.
> Now as I am sure about my built structure. I want to perform calculations at 
> specific pH. How do I do this in Amber?
> Thanks
> 
> 
> 
> ________________________________
> From: Bill Ross <ross.cgl.ucsf.EDU>
> To: amber.ambermd.org
> Sent: Fri, July 23, 2010 5:36:47 PM
> Subject: Re: [AMBER] question about bond command
> 
>> How about one of my residues that has 4 bonds, Is 
>> it a must to use connecX, or bond command should give the right results?
> 
> ConnectX refers to a state that you confer on an atom,
> where X is 0,1,2..
> 
> Bond is a command that connects 2 atoms with connectX
> state. 
> 
> Bill
> 
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Received on Sat Jul 24 2010 - 22:30:04 PDT