Re: [AMBER] Cyclic peptides in Amber?

From: Alexander Izvorski <>
Date: Sun, 6 Sep 2020 15:14:29 -0700

Thanks Bill and David - That got me on the right track. Both these ways
worked, but what I ended up doing eventually is a little different from
either suggestion, using clearPdbResMap. Hopefully may help anyone else
who has a similar system to simulate.

I put the non-cyclic protein(s) in one pdb, and the cyclic peptide in
another, then

> source leaprc.protein.ff14SB
> mol1 = loadpdb noncyclic.pdb
> clearPdbResMap
> mol2 = loadpdb cyclic.pdb
> bond mol2.1.N mol2.10.C
> mol = combine { mol1 mol2 }

... and proceeded as usual from there.

For Amber devs: I think the res map should not assign N/C terminal variants
to amino acids which are properly peptide bonded, just because they're the
first/last one in the pdb; also pdb4amber probably shouldn't delete peptide
bonds. In any case, everything is working good for my practical problem.


On Sat, Sep 5, 2020 at 11:41 AM David A Case <> wrote:

> 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 Sun Sep 06 2020 - 15:30:02 PDT
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