Re: [AMBER] how does tleap choose missing side chain conformations

From: Carlos Simmerling <>
Date: Mon, 1 Feb 2021 06:23:01 -0500

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 <>

> 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.
> Assistant Professor,
> Department of Pharmacy,
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Received on Mon Feb 01 2021 - 03:30:02 PST
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