Re: [AMBER] constant ph md

From: David A Case <>
Date: Thu, 12 Aug 2021 07:10:41 -0400

On Thu, Aug 12, 2021, Abhik Ghosh Moulick wrote:

>Recently I am trying to perform constant pH md simulation in implicit
>solvent. During the building of input structure, I found that in tleap
>file information regarding the disulfide bond is added.

Can you be specific here: what is the exact reason that you conclude that
"file information regarding the disufide bond is added"? What was your
tleap input?

If there is a CONECT record in the input pdb file, tleap will use that to
create disulfide bonds. Also, the pdb4amber program will look for disulfide
bonds, and create the necessary CONECT records.

>Secondly if I want to run a constant ph on another protein which have
>disulfide bond, but I need to titrate only ASP and GLU, then does disulfide
>bond information is needed to mention in tleap file?

You need to get disufide bonds created in some manner, whether you are
running constant pH simulations or not.

>I am new to amber so any kind of help is highly appreciable.

Gain some experience with standard MD runs before trying constant pH.


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Received on Thu Aug 12 2021 - 04:30:02 PDT
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