Re: [AMBER] aMD- alphaD- what does solute residues mean?

From: Elvis Martis <elvis.martis.bcp.edu.in>
Date: Wed, 29 Nov 2017 11:45:57 +0000

HI,
I would consider whole of the system under study as solute residue, which includes your protein, cofactors and ligand (if any).
Hope this helps.

Best Regards
Elvis Martis
Mumbai, INDIA.

________________________________________
From: Thakur, Abhishek <axt651.miami.edu>
Sent: 29 November 2017 02:06
To: amber.ambermd.org
Subject: [AMBER] aMD- alphaD- what does solute residues mean?

Hi everyone,


I was going through the amber tutorial for aMD and have found one term solute residues.


alphaD: Alpha(dih)=(1/5)*(4kcal mol-1 residues-1 * 58 solute residues)


If I have protein, cofactor and peptide will everything considered as a solute residue? or only protein residues are called solute residues?


http://ambermd.org/tutorials/advanced/tutorial22/section2.htm


<http://ambermd.org/tutorials/advanced/tutorial22/section2.htm>


<http://ambermd.org/tutorials/advanced/tutorial22/section2.htm>

Thanking you,<http://ambermd.org/tutorials/advanced/tutorial22/section2.htm>

-Abhishek
<http://ambermd.org/tutorials/advanced/tutorial22/section2.htm>

AMBER Advanced Tutorial 22 - Accelerated Molecular ...<http://ambermd.org/tutorials/advanced/tutorial22/section2.htm>
ambermd.org
Accelerated Molecular Dynamics run using Amber - Section 2




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Received on Wed Nov 29 2017 - 04:00:03 PST