[gmx-users] Simulations of non standard nucleic acids

Mark Abraham mark.j.abraham at gmail.com
Wed Mar 2 11:21:00 CET 2016


If you have a whole molecule topology, then existing conversion tools for
Amber topologies might be enough. If you need to use tools like pdb2gmx,
then you need to write an .rtp file, whose format is described in the
GROMACS documentation.


On Wed, Mar 2, 2016 at 11:19 AM Prayagraj Fandilolu <fprayagraj at gmail.com>

> Hi Gromacs Users,
> I am trying to simulate a RNA system with some modified nucleic acid
> bases.. The problem is to generate the topologies for them.
> Can anyone tell me how to generate them?? I am having the topologies in
> amber prep format... How can i be able to use them in gromacs?? Further,
> which forcefield would be better??
> I am new to gromacs hence additional suggestions are welcome....
> Thanks in advance.......
> Mr. Prayagraj Fandilolu
> Research Scholar,
> Structural Bioinformatics Unit
> Department of Biochemistry
> Shivaji University, Kolhapur - 416004
> (MS) India
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