Re: [AMBER] question about bond command

From: Philippe Pinard <pp_amber17.yahoo.com>
Date: Sun, 25 Jul 2010 20:52:21 -0700 (PDT)

Hello

Thanks for the email.
My aim is performing explicit solvent calculations.
My residues are not the conventional amber ones. I have a macromolecule that is
composed of reidues I built with antechamber. I know from titration experiments
what would be the residues at different pHs. My question how to build a new
structure for each protonation state, i.e a given pH?

My other question now is how to use ptraj to compute radius of gyration, I cant
find details in the manual about it.
Thanks in advance for your help.
Regards




________________________________
From: Jason Swails <jason.swails.gmail.com>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Sun, July 25, 2010 6:04:18 AM
Subject: Re: [AMBER] question about bond command

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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> 
> 
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Received on Sun Jul 25 2010 - 21:00:04 PDT