Hi,
On Tue, Jun 22, 2021 at 2:38 PM Sruthi Sudhakar
<sruthisudhakarraji.gmail.com> wrote:
> attaching the pdb here. Other than manually editing the pdb text file, is
> there a way to change the residue names?
You can use the cpptraj 'change' command to change residues in a mask
to a certain name. For example, to change residues numbered 1 and 3 to
"C" you would do:
change resname from :1,3 to C
The advantage of doing it via cpptraj is that PDBs written by cpptraj
correspond very well to PDB standards (largely thanks to comments from
DAC).
Hope this helps,
-Dan
>
>
> Regards,
> Sruthi Sudhakar
>
>
> On Sat, Jun 19, 2021 at 3:28 PM Petr Stadlbauer <petr.stadl.gmail.com>
> wrote:
>
> > 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
> > > >
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Received on Wed Jun 23 2021 - 06:30:02 PDT
