Hi,
I would like to use Amber20 with ff19SB for proteins and OL3 for RNA to simulate some RNA protein complexes. There is, however, some bug with RNA which represents itself in the following ways:
1) If you do not load the ff19SB force field in tleap and build the system of only RNA with loading only OPC waters and OL3, the simulations crash (no specific error message, but the system blows up).
2) If you load ff19SB in tleap and do the same simulations run, but everything is "frozen" as if some constraints are in place, not even ions move anywhere.
3) The freezing happens even with a protein included.
I am using the Langevin thermostat and Monte Carlo barostat, and using input files that function without issues for the protein only. Including the RNA causes this weird behavior. The RNA structure is from previous simulations with ff14SB and OL3, so it should not have any major issues causing the crashing.
I hope you can help me get my simulations running.
Cheers,
Piia Kokkonen
--
Piia Kokkonen, Ph.D. (Pharmacy)
Project Researcher
University of Eastern Finland | UEF | School of Pharmacy
Kuopio Campus | Canthia
Yliopistonranta 1 C | P.O. BOX 1627 | 70211 Kuopio
+358 50 548 8376 | piia.kokkonen.uef.fi
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Received on Wed Oct 28 2020 - 04:00:03 PDT
