[gmx-users] Simulations of non standard nucleic acids

Prayagraj Fandilolu fprayagraj at gmail.com
Wed Mar 2 11:18:37 CET 2016

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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