[gmx-users] setting up simulation with mixed chain (nucleotide + amino acid)

Tomek Wlodarski tomek.wlodarski at gmail.com
Mon Nov 18 14:26:32 CET 2013


Hi,

I would like to run simulation of short peptide (nascent chain) bound to
tRNA (in amber ff).
Do gromacs supports chains which have both protein and nucleic acid
components?
I have problem with termini of this chain:
gromacs is trying to find 3'- terminus of RNA - but it can't because
terminus of the chain is amino acid type...
I know that I have to parametrize bond between nucleotide and protein.
Should I change type of this chain to either RNA or protein - e.g. by
creating special class in aminoacid.rtp which includes nucleotides (with
new names)?
I would be very grateful for any suggestions.
Thank you.
Best,

tomek


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