Re: [AMBER] OHE residue and crashing

From: Piia Kokkonen <>
Date: Tue, 12 May 2020 06:04:31 +0000


Thanks for the suggestions. I will see if I can get somehow away with this, and I hope at some point some decent solution comes to this phosphate.

Should the monophosphate.lib be in the tleap libraries or do I need to download it from somewhere?


Piia Kokkonen, Ph.D. (Pharmacy)
University of Eastern Finland
School of Pharmacy
P.O. BOX 1627
70211 Kuopio
Phone: +358 50 548 8376
From: Christina Bergonzo <>
Sent: Monday, May 11, 2020 15:48
To: AMBER Mailing List <>
Subject: Re: [AMBER] OHE residue and crashing
I am going to be not much help here, as I've never encountered this problem
- haven't run any RNA simulations with 5'phosphates!
Dave's suggestions all seem logical to me.
After determining that this is your problem, I'd first try adding LJ
parameters to the hydrogen, then looking at the monophosphate.lib
parameters, and finally just taking the timing hit and run without hydrogen
mass partitioning at 2 fs and see how it goes (I'd probably submit this
first and then work on the other two, just because it's already
minimized/equilibrated and you'd only have to change the input file).
Good luck, sorry there are no clear answers here :-/
On Sun, May 10, 2020 at 2:28 PM David A Case <> wrote:
> 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.
> ....dac
> _______________________________________________
> AMBER mailing list
Christina Bergonzo
Research Chemist
Biomolecular Measurement Division, MML, NIST
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Received on Mon May 11 2020 - 23:30:02 PDT
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