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