Dear Sruthi,
first make sure your structure is not degraded anymore. What happened
to your structure reminds me of what happens when one changes residue
or atom names and fails to keep them in the same columns. It results
in a shift in the rest of the line and leap (or other visualization
software) loads the coordinates incorrectly. So add or remove blank
spaces where needed. There could be some other errors with the names
and types, but try to resolve the structural problem first.
Regards,
Petr
so 19. 6. 2021 v 9:37 odesílatel Sruthi Sudhakar
<sruthisudhakarraji.gmail.com> napsal:
>
> Thank you sir for the reply. I have followed the following methodology but
> faced some issues in the preparation of the structure. Initially I have
> modified the all_prot_nucleic10.lib file by changing the atom types for
> residues DCP (CH+), D3C (3’-terminal CH+) and D5C (5’-terminal CH+) in the
> following way:
> "C5'" "CI" -> "C5'" "CJ"
> "C3'" "CT" -> "C3'" "C7"
> "C6" "CM" -> "C6" "C1"
> "C5" "CM" -> "C5" "C1"
> But in the second stage when I try to change the residue name in the pdb
> file, the structure seems to be degraded. I opened the pdb text file and
> manually changed the DC to DCP/D3C/D5C and saved it too. But after this
> change, when I opened the structure in Pymol to visualize the same, it
> seems broken and even in leap it got errors. Is there a mistake in the
> methodology of Changing the residue names.
> Regards,
> Sruthi Sudhakar
>
>
> On Wed, Feb 10, 2021 at 11:04 PM Petr Stadlbauer <petr.stadl.gmail.com>
> wrote:
>
> > Dear Sruthi,
> >
> > > Dear all,
> > >
> > > I would like to know how the preparation of i-motifs ( semiprotonated
> > C-C+)
> > > base pairs can be prepared.
> >
> > Take your input structure file and designate one of the cytosines in
> > each CC+ pair with a special residue label, which would correspond to
> > your parameter files for C+.
> >
> > > We could add a hydrogen on to the nitrogen to
> > > make it protonated,but how different would be the forcefield preparation.
> >
> > You need to load parameters for C+, which have RESP charges calculated
> > for C+ and parameters for the angles including the hydrogen on N3.
> >
> > > Typically for G quadruplexes we could use the OL15 force field, what
> > would
> > > be the case with i-Motifs? Also since there is a semiprotonated cytosine,
> > > do we need any other parametrization to continue with the topology
> > > generation?
> >
> > You can use OL15 for i-motif for sure. You may try to use slightly
> > obsolete bsc0 parameters for C+ provided in amber. I am not sure
> > whether it varies among amber versions, but in amber18 you can find
> > these parameters in files called all_prot_nucleic10.lib and
> > frcmod.protonated_nucleic, which you need to load. The residue label
> > corresponding to DNA C+ is DCE then.
> >
> > > Thank you for any guidance you can provide.
> > >
> > > Regards,
> > > Sruthi
> >
> > Regards,
> > Petr
> >
> > > _______________________________________________
> > > 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
> >
> _______________________________________________
> 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
Received on Sat Jun 19 2021 - 03:00:02 PDT
