Dear All,
I wish to perform CpHMD simulations on a protein of my interest at pH: 3,
4, 5, 6, 7, 8, 9, 10, 11 and 12.
I have gone through the related tutorial (
http://ambermd.org/tutorials/advanced/tutorial18/index.htm), wherein they
have titrated the acidic residues only.
I would like to titrate all residues for the pH range 3-12, and for that,
do I have to just change the name of residues at once (Aspartate--AS4,
Glutamate--GL4, Histidine--HIP, Tyrosine--TYR, Lysine--LYS) to create top
and crd files, as given in the tutorial. After that, do I have to utilize
these top and crd files to perform simulations for pH range 3-12?
What about other residues, such as Arginine, Serine, Aspartic and Glutamic
acid? Do we need some specific modified names for these residues too?
Is this single top and crd files can be used to titrate the residues even
for entire pH range, i.e. from acidic to alkaline?
In summary, I have a protein which I downloaded from RCSB, I want to see
the structural changes of this protein at varying pH levels (3-12 range). I
would be very grateful if you could offer some help or guidance in this
regard.
Thank you!
Best Regards,
Jac
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Received on Tue Jun 25 2019 - 07:00:05 PDT
