Re: [AMBER] question about bond command

From: Jason Swails <jason.swails.gmail.com>
Date: Sun, 25 Jul 2010 01:04:18 -0400

Hello,

You can either use constant pH MD in implicit solvent if you don't know HHS proper protonation states of the titratable residues, or you can predetermine the dominant protonation states of the titratable residues and run MD with those specified states. The different titratable residues have different residue names for the different protonation states as described in the manual for ambertools I believe. For example, deprotonated aspartate is ASP, protonated aspartic acid is ASH, and the 4-proton titratable aspartate is AS4.

Hope this helps,
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 - 22:30:03 PDT