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

From: Elvis Martis <>
Date: Wed, 29 Nov 2017 11:45:57 +0000

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 <>
Sent: 29 November 2017 02:06
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?



Thanking you,<>


AMBER Advanced Tutorial 22 - Accelerated Molecular ...<>
Accelerated Molecular Dynamics run using Amber - Section 2

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