You can also make a leaprc that overrides the auto-end-replacement rule,
copy the default to your working dir and delete that rule set.
Bill
On 9/5/20 1:06 AM, Bill Ross wrote:
> 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
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Received on Sat Sep 05 2020 - 01:30:03 PDT
