Dear All,
I want to use a polarizable force field for MD simulation of a protein with
non-standard residues and cofactors.
If possible, can you please suggest how these are generally used in Amber18
or Amber20?
I can't find a tutorial, archive message that is specific for this, nor
does the manual or FF-page contain information with which one can easily
identify availability, usage and current limitations. Section 3.12.4 does
mention a 2002 polarizable FF, but it under the obsolete FF section 3.12
and thus probably not recommended by developers, is it?
Contributions to Amber does mention "Jim Caldwell and Piotr Cieplak,
primary developers of the original Amber polarizable force fields".
But it doesn't say much about which these are and how to use/call them in
tleap (if these are not the obsolete ones).
Thus I'm guessing that this would need some development/validation on case
to case basis and thus not trivial or a routine task in Amber.
Please help me understand the current recommendations in Amber and
state-of-the-art.
Looking forward to valuable suggestions from the list.
Thank you and best regards.
--
Regards,
Dr. Vaibhav A. Dixit,
Visiting Scientist at the Manchester Institute of Biotechnology (MIB), The
University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
AND
Assistant Professor,
Department of Pharmacy,
▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄▄
Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
India.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
http://www.bits-pilani.ac.in/pilani/vaibhavdixit/profile
https://www.linkedin.com/in/vaibhav-dixit-b1a07a39/
ORCID ID: https://orcid.org/0000-0003-4015-2941
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
P Please consider the environment before printing this e-mail
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Feb 07 2021 - 02:30:02 PST
