Re: [AMBER] Explicit water molecules in MMPBSA.py: OPC vs TIP3P

From: Lennart Gundelach <L.Gundelach.soton.ac.uk>
Date: Thu, 14 Oct 2021 07:58:38 +0000

Hi Ray,

Sorry for late reply, just found this in my spam folder today.

The structures look fine.

The problem seems to be that MM-PBSA.py can’t handle the 4-point water model. If I strip out all the 4th “atom” form the OPC model, leaving only the two Hydrogens and the Oxygen, from the input files (obviously this is a terrible idea), MM-PBSA.py runs without problems, just give pretty silly energies.

I have re-run my MD simulations with ff19SB + TIP3P and these trajectories cause no issues with MM-PBSA.py.

Since ff19SB+TIP3P is not recommended, I am now running Md for ff19SB+OPC3 which is also a three point water model and should thus work.

Thanks,

Lennart

From: Ray Luo <rluo.uci.edu>
Date: Wednesday, 8 September 2021 at 17:36
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Explicit water molecules in MMPBSA.py: OPC vs TIP3P
CAUTION: This e-mail originated outside the University of Southampton.

Lennart,

Just a suggestion to get the debugging going ... Have you tried to
visualize the stripped prmtop/traj files in VMD or other similar
programs to see whether there is any bonding issue with the remaining
water molecules?

All the best,
Ray 
--
Ray Luo, Ph.D.
Professor of Structural Biology/Biochemistry/Biophysics,
Chemical and Materials Physics, Chemical and Biomolecular Engineering,
Biomedical Engineering, and Materials Science and Engineering
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
On Wed, Sep 8, 2021 at 4:35 AM Lennart Gundelach
<L.Gundelach.soton.ac.uk> wrote:
>
> Hi,
>
> I have been running MMPBSA.py with a couple of explicit waters defined as part of the complex. This worked fine when working with trajectories (and .prmtop) that had been generated using ff14SB + TIP3P but seems to no longer work when using trajectories generated with ff19SB + OPC.
>
> Both the complex and receptor calculations yield ‘nan’ for VdW and EEL while the ligand calculation works just fine (since it has not waters). The only change made to setup is new trajectories generated with ff19SB + OPC instead of ff14SB + TIP3P.
>
> Could it be, that due to the 4 point setup of OPC, MMPBSA.py does not know how to handle the  4th point, which does not directly correspond to an atom?
>
> From topology files:
> TIP3P: OW HW HW
> OPC: OW HW HW EP
>
> Could this be the issues? Anny suggestions how to proceed?
>
> Thanks,
>
> Lennart
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Received on Thu Oct 14 2021 - 01:00:03 PDT
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