Re: [AMBER] Preparation of i-Motif structures

From: Sruthi Sudhakar <>
Date: Sat, 19 Jun 2021 13:06:31 +0530

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.
Sruthi Sudhakar

On Wed, Feb 10, 2021 at 11:04 PM Petr Stadlbauer <>

> 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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> >
> >
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Received on Sat Jun 19 2021 - 01:00:02 PDT
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