[AMBER] how does tleap choose missing side chain conformations

From: Vaibhav Dixit <vaibhavadixit.gmail.com>
Date: Mon, 1 Feb 2021 09:21:51 +0530

Dear All,
After performing MD and traj analysis, I ran into this question for which I
can't find a clear answer in archives or manual/tutorials.
Thus can you please help me understand, which aspects/parameters are
considered by tleap while choosing the side-chain conformations when only
backbone coordinates are present in a protein PDB.
Does it consider the simpler Ramachandran-allowed/disallowed regions and
steric/electrostatic factors or more rigorous probability of finding a
particular side-chain conformation extracted by analyzing a large number of
structures from the PDB database or something else? Is it possible to
estimate possible conformers and then instruct tleap to choose one
conformer over the other?
I can imagine that this choice would depend on the existing info and type
of analysis to be performed. Nonetheless, are there other common aspects
which are important and applicable to the majority of proteins?

Your valuable suggestions will help me perform further analysis with
confidence and in a proper context.
Looking forward to valuable suggestions from the list.
thank you and best 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.
Assistant Professor,
Department of Pharmacy,
Birla Institute of Technology and Sciences Pilani (BITS-Pilani),
VidyaVihar Campus, street number 41, Pilani, Rajasthan 333031.
Phone No. +91 1596 255652, Mob. No. +91-7709129400,
Email: vaibhav.dixit.pilani.bits-pilani.ac.in, vaibhavadixit.gmail.com
ORCID ID: https://orcid.org/0000-0003-4015-2941
P Please consider the environment before printing this e-mail
AMBER mailing list
Received on Sun Jan 31 2021 - 20:00:02 PST
Custom Search