Right, thank you very much Thomas !
For the moment I could resolve the issue by just removing the second
chain (a short peptide) bound to the protein from the complex while
keeping the terminal TER. In that case, ain't no problems with the C
and N ends.
Anyway, could you please suggest some modification of my tleap script
in order that I could N and C termini automatically ?
Many thanks in advance
Cheers
Enrico
Il giorno mer 5 lug 2023 alle ore 13:06 Steinbrecher, Thomas
<thomas.steinbrecher.roche.com> ha scritto:
>
> Hi Enrico,
>
> could you load your protein in xleap and use the "edit prot" command (preferably before adding the water box)? If there is a long bond you should see it then, but if leap gives no warning, maybe this is just a visualisation issue from switching to another software. Anyway, a quick minimization should definitely show if Amber thinks there is a bond or not...
>
> Independent from this issue, it may be worth adding capping groups to your system anyway, depending on if the termini you have in your molecule are real or just the end of the structurally resolved part of your proteins. The position of the termini in a PDB may not be the actual termini of the crystallized polypeptide, which may not be the actual termini of the wild type sequence which may not be the termini in the construct used for the assay you maybe compare your results to.
>
> Kind Regards,
>
> Thomas
>
> On Wed, Jul 5, 2023 at 11:56 AM Enrico Martinez <jmsstarlight.gmail.com> wrote:
>>
>> Normally yes there is a TER between the both chains in the initial pdb
>> as well as a TER in the end.. :-)
>>
>>
>> here is the tleap log
>>
>> /teLeap: Warning!
>> Converting N-terminal residue name to PDB format: NGLY -> GLY
>>
>> /teLeap: Warning!
>> Converting C-terminal residue name to PDB format: CGLY -> GLY
>>
>> /teLeap: Warning!
>> Converting N-terminal residue name to PDB format: NASP -> ASP
>>
>> /teLeap: Warning!
>> Converting C-terminal residue name to PDB format: CARG -> ARG
>>
>> Checking Unit.
>> Building topology.
>> Building atom parameters.
>> Building bond parameters.
>> Building angle parameters.
>> Building proper torsion parameters.
>> Building improper torsion parameters.
>> total 672 improper torsions applied
>> Building H-Bond parameters.
>> Incorporating Non-Bonded adjustments.
>> Not Marking per-residue atom chain types.
>> Marking per-residue atom chain types.
>> (Residues lacking connect0/connect1 -
>> these don't have chain types marked:
>>
>> res total affected
>>
>> CARG 1
>> CGLY 1
>> NASP 1
>> NGLY 1
>> WAT 37077
>>
>>
>> mb this is just a visual effect ?
>>
>> Il giorno mer 5 lug 2023 alle ore 11:41 Steinbrecher, Thomas
>> <thomas.steinbrecher.roche.com> ha scritto:
>> >
>> > Hi Enrico,
>> >
>> > does your input PDB contain the right "TER" lines between separate protein chains? Otherwise, leap may consider this as one continuous protein chain but should warn you about any "long bonds" that are created.
>> >
>> > Kind Regards,
>> >
>> > Thomas
>> >
>> > On Wed, Jul 5, 2023 at 11:34 AM Enrico Martinez via AMBER <amber.ambermd.org> wrote:
>> >>
>> >> Dear Amber users !
>> >>
>> >> I am preparing system of water soluble protein using tleap with the
>> >> following script :
>> >>
>> >> source leaprc.protein.ff19SB
>> >> source leaprc.water.opc
>> >> prot = loadpdb input.pdb
>> >> addIons prot Cl- 0
>> >> addIons prot Na+ 0
>> >> setbox prot centers
>> >> solvateoct prot TIP3PBOX 20.0
>> >> savepdb output.pdb
>> >> saveamberparm output.prmtop output.prmcrd
>> >> quit
>> >>
>> >>
>> >> Briefly, everything works OK but in the output.pdb I see that the N
>> >> and C terminus of the proteins are connected by the artificial
>> >> covalent bond despite the large physical distance between them... I
>> >> performed a short MD simulation for the system and extracted snapshots
>> >> after it and in pymol I see the same thing.
>> >>
>> >> Should the C and N parts be capped to prevent this bug ? If yes, could
>> >> you please suggest the modification of my tleap script in order that
>> >> the first and the last residues would be automatically capped without
>> >> explicit definition of the amino acid ?
>> >>
>> >> Many thanks in advance
>> >>
>> >> Cheers
>> >>
>> >> Enrico
>> >>
>> >> _______________________________________________
>> >> AMBER mailing list
>> >> AMBER.ambermd.org
>> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >
>> >
>> >
>> > --
>> > Dr. Thomas Steinbrecher
>> > Principal Scientist CADD
>> >
>> > Roche Pharma Research and Early Development
>> > Roche Innovation Center Basel
>> > F. Hoffmann-La Roche Ltd
>> > Bldg. 092/3.92
>> > Grenzacherstrasse 124
>> > 4070 Basel
>> > Switzerland
>> >
>> > Phone +41 61 682 1319
>> > mailto: thomas.steinbrecher.roche.com
>
>
>
> --
> Dr. Thomas Steinbrecher
> Principal Scientist CADD
>
> Roche Pharma Research and Early Development
> Roche Innovation Center Basel
> F. Hoffmann-La Roche Ltd
> Bldg. 092/3.92
> Grenzacherstrasse 124
> 4070 Basel
> Switzerland
>
> Phone +41 61 682 1319
> mailto: thomas.steinbrecher.roche.com
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Received on Wed Jul 05 2023 - 09:00:02 PDT
