Hello Jacob,
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?
Yes. But make sure to also specify the residues you want to titrate in your cpinutil.py command. Amber reads the list of which residues to titrate from the CPIN file.
What about other residues, such as Arginine, Serine, Aspartic and Glutamic
acid? Do we need some specific modified names for these residues too?
You may use the regular names for the residues you don't wish to titrate.
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?
Yes, as long as you have selected all residues that are active in the pH range you chose.
Here is another nice CpHMD tutorial you can check: http://jswails.wikidot.com/explicit-solvent-constant-ph-md
I hope this helps,
All the best,
Vinícius Wilian D. Cruzeiro, PhD
Postdoctoral Researcher
San Diego Supercomputer Center
Department of Chemistry and Biochemistry
University of California, San Diego
Voice: +1(858)246-5584
________________________________
From: jacob wick <jacobwick.la.gmail.com>
Sent: Tuesday, June 25, 2019 6:56 AM
To: AMBER Mailing List
Subject: [AMBER] Correct procedure to perform CpHMD simulations
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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jun 25 2019 - 11:00:03 PDT
