Hi Bill - Thanks! It seems that would just create an extended chain with
that sequence. I'd like to use the coordinates from the pdb file - these
cyclic peptides are made in PyMol now as a test, but for production I'd be
running Rosetta -> Amber.
Is there some way to load a cyclic peptide from pdb? (or fix it up after
it's loaded)
Best,
Alex
On Sat, Sep 5, 2020 at 12:59 AM Bill Ross <ross.cgl.ucsf.edu> wrote:
> loadpdbusingsequence
>
>
> On 9/4/20 10:52 PM, Alexander Izvorski wrote:
> > 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> --
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Received on Sat Sep 05 2020 - 01:30:02 PDT
