AMBER Archive (2007)

Subject: Re: AMBER: phe-phe molecule

From: David A. Case (case_at_scripps.edu)
Date: Wed Feb 28 2007 - 12:03:49 CST

On Tue, Feb 27, 2007, deepti nayar wrote:
>
> when I load the dipeptide in xleap, there i see a difference in the atom
> names since both the propgrams must be following some diffrenet atom
> name conventions.

In LEaP, just use the "desc PHE" command to get the atom names Amber uses in
its libraries. Then edit your mol2 file so that the atom names match what
Amber expects.

>
> when i load the phe-phe dipeptide in xleap, it tells me some wrong
> torsional angles etc.

We need details here: what were the commands you actually gave to LEaP?
What was the error message that resulted? Since we don't know either one of
the these, it is not possible to provide much useful advice.

...dac

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