Thanks for the clarification and suggestions.
I will try the Chimera option and get back in case I have
additional questions.
Best regards
On Mon, Feb 1, 2021 at 4:53 PM Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> Leap does not a make any attempt to find a favorable conformation. It
> builds missing atoms the same way every time, according to Z matrix data in
> the library files. You can change that during leap using the impose
> command. Leap is not intended to be for model building, and its really
> better to give it complete coordinates if you are concerned about initial
> model. I often use Chimera, which will search rotamer libraries and check
> for clashes. Other programs may provide similar features. Then load the
> resulting coordinates into leap (usually using pdb4amber first).
>
> On Sun, Jan 31, 2021, 10:52 PM Vaibhav Dixit <vaibhavadixit.gmail.com>
> wrote:
>
> > 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.
> >
> > --
> >
> > 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
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--
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
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Received on Tue Feb 02 2021 - 03:30:02 PST
