loadpdbusingsequence lets you override the residue type, then you can
add the bond in leap.
Bill
On 9/5/20 1:05 AM, Alexander Izvorski wrote:
> 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
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>> --
>> Phobrain.com
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
Phobrain.com
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Sep 05 2020 - 01:30:03 PDT
