Re: [AMBER] Fwd: Constant pH MD simulation

From: David A Case <>
Date: Wed, 10 Nov 2021 14:54:40 -0500

On Wed, Nov 10, 2021, Divya Rai wrote:

>Now, I am using a basic solvent pH(~8). For my system, there are 2 CYS
>residues involved in a disulphide linkage (and thereby are present in the
>pdb with the resname "CYX"). So, do I need to change the resnames
>accordingly (i.e. "CYS") so as to be able to titrate them or should I keep
>them as it is (i.e. "CYX").

Do you have reason to think that the disulfide bonds will break at pH 8?
This would be unusual. Converting from CYX to CYS is an oxidation/reduction
conversion, not a proton titration one. If you wish to model the CYS
titration behavior after the disulfides are broken, then (indeed) you need
to change CYX to CYS. But be sure that is really what you want to do.


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Received on Wed Nov 10 2021 - 12:00:02 PST
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