Re: [AMBER] Optimization of geometry in xleap

From: Bill Ross <>
Date: Wed, 29 May 2019 23:36:14 -0700

xleap can be used to build small molecules. It only knows the
hybridization of the atoms, so the geometries it produces are sterically
unaware, but with small molecules this is easy to see and fix. I like
the ability to just allow selected atoms to relax. It is rarely used in
practice, I believe, since better UI's exist for general building of
structure, but I think it is the original core of leap, and was maybe
the only part I didn't rework as second 'owner'.


On 5/29/19 11:21 PM, Shilpa Gupta wrote:
> Dear Amber Users,
> Is it possible to build an anion and optimization of its geometry in Xleap?
> As leap takes the molecule with its complete valence, so if i will give -COO
> - (carboxylate group ) then it will try to complete valence of O atom and
> in result some vague structure is displayed in VMD (in pdb file format).
> After this i want to generate the charges for the corresponding atoms.
> One thing i want to ask that the charge derivation of the anion is possible
> in R.E.D tools. Any reply would be helpful. Thanks in advance.
> Shilpa Gupta
> University of Delhi
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Received on Thu May 30 2019 - 00:00:01 PDT
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