[AMBER] Cyclic peptides in Amber?

From: Alexander Izvorski <aizvorski.gmail.com>
Date: Fri, 4 Sep 2020 22:52:52 -0700

Dear Amber users,

I'm trying to load a cyclic peptide in Amber using tleap. This is made in
PyMol, just by using the "Build" menu. It has a head-to-tail amide bond,
the N of the first residue is bonded to the C of the last residue.

What happens:
1. If I save this from PyMol as a pdb with "Write CONECT records for all
bonds, and load it in tleap, the amide bond is there, but the end residue
types become NSER and CPRO (instead of normal SER and PRO as they probably
should be), and tleap adds an OXT atom (and extra hydrogens).

That results in a rather strange molecule with too many bonds:

> mol = loadpdb cyctest1.pdb
  Added missing heavy atom: .R<CPRO 10>.A<OXT 15>

> desc mol.1.N
  Bonded to .R<NSER 1>.A<H1 2> by a single bond.
  Bonded to .R<NSER 1>.A<H2 3> by a single bond.
  Bonded to .R<NSER 1>.A<H3 4> by a single bond.
  Bonded to .R<NSER 1>.A<CA 5> by a single bond.
  Bonded to .R<NSER 1>.A<H 14> by a single bond.
  Bonded to .R<CPRO 10>.A<C 13> by a single bond.

> desc mol.10.C
  Bonded to .R<CPRO 10>.A<CA 11> by a single bond.
  Bonded to .R<CPRO 10>.A<O 14> by a single bond.
  Bonded to .R<CPRO 10>.A<OXT 15> by a single bond.
  Bonded to .R<NSER 1>.A<N 1> by a single bond.

2. If I save the pdb file from PyMol without "Write CONECT", or if I run it
through pdb4amber, the head-to-tail amide bond isn't there, and the
residues are also NSER and CPRO. I think pdb4amber removes all CONECT
records except disulfides.

How do I make the first/last residue types to be SER and PRO instead of
NSER and CRPO? How do I prevent the OXT from being added? (or remove it
after it's added?)

Many thanks,
Alex Izvorski
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Received on Fri Sep 04 2020 - 23:00:03 PDT
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