Re: [AMBER] Preparation of i-Motif structures

From: Petr Stadlbauer <>
Date: Wed, 10 Feb 2021 18:34:15 +0100

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


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Received on Wed Feb 10 2021 - 10:00:02 PST
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