Re: [AMBER] OHE residue and crashing

From: David A Case <>
Date: Sun, 10 May 2020 14:28:15 -0400

On Fri, May 08, 2020, Piia Kokkonen wrote:
>I am trying to run RNA simulations with 5' phosphates (and without)
>using the OL3 force field and Amber18. I can generate files and run
>some minimization with both systems, but the system with OHE (the 5'
>phosphate) will crash when I get to production simulations.

You can check your geometries right beore the crashes, but I'm guessing
the proton on OHE is getting too close to one of the other oxygen atoms
on the same phopshate. You could try using the "lmod" action in parmed
to add LJ parameters to the HO atoms on the phosphate.

We also have a monophosphate.lib library, that puts a 5' phopshpate on
the terminal nucleotides when loaded. It's not clear that this will
solve the problem with the hydrogen (if that is indeed your problem),
but it might.

This is a frustrating problem, since (if my diagnosis is correct) it has
been fixed (and problem un-fixed) multiple times. I'm hoping that
others on the email list (Christina?) can chime in the more specific
advice. I think these "fixes" tend to get done in an ad-hoc way, and
never really incorporated to the standard workflows.


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Received on Sun May 10 2020 - 11:30:03 PDT
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