Re: [AMBER] Cyclic peptides in Amber?

From: David A Case <>
Date: Sat, 5 Sep 2020 14:40:52 -0400

On Fri, Sep 04, 2020, Alexander Izvorski wrote:
>I'm trying to load a cyclic peptide in Amber using tleap.

There is more than one way to do this, but here's what I do: make a copy of
$AMBERHOME/dat/leap/cmd/leaprc.protein.ff19SB (or whatever protein force field
you want.). In the copy, remove the "addPdbResMap" section, which is the code
that converts terminal residues. Source that leaprc file instead of the
original one, then proceed as usual.

....hope this helps....dac

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Received on Sat Sep 05 2020 - 12:00:01 PDT
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