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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Received on Sat Sep 05 2020 - 01:00:02 PDT
