Re: [AMBER] Amber20 and RNA simulations

From: Piia Kokkonen <piia.kokkonen.uef.fi>
Date: Wed, 28 Oct 2020 12:22:05 +0000

Hi,

Thanks for a quick answer. I included my files in this rar file:
https://www.dropbox.com/s/g8abpe060kbes5e/onlymir.rar?dl=0

The tleap input I put in that order (with or without the line of ff19SB).
The prodout.txt should have the mdin input file for the production and the energy/volume etc information (which does not appear very unusual).
The stripped* files contain the first few frames of the output trajectory where I noticed that it behaves weirdly.

Just let me know if anything else is needed.

Cheers,
Piia 

--
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
________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Wednesday, October 28, 2020 13:58
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Amber20 and RNA simulations
On Wed, Oct 28, 2020, Piia Kokkonen wrote:
>
>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).
Can you provide a small example that illustrates the problem?  There are
many, many things we don't know about what you are doing, such as:
    a. what were the tleap commands you used (especially the order of
        loading files)
    b. What simulation program did you use?  What parameters were in the
        mdin input file?
You might also check to see if a different water model gives the same
error.
>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.
How did you decide that everything was "frozen"?  Was it from visually
watching the trajectory?  Do the temperature and density profiles look
ordinary?
Basically, we need to be able to reproduce the problem in order to
provide advice.
....dac
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Received on Wed Oct 28 2020 - 05:30:02 PDT
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