[gmx-users] Regarding siRNA simulation.

Anurag Dobhal anurag.dobhal at nano-medicine.co.in
Sun Sep 28 13:36:40 CEST 2014

I am simulating an RNA molecule in which  first residue has a 5'-PO4 cap,
which is uncommon. I am adding the atoms and bond parameters in the .rtp
files in the existing force field directories but these parameters are not
getting saved. I am using Amber 99 force field and i am making changes in
the rna.rtp file.

How can i make these changes possible.
Do I need to write new .rtp file.

please help



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