I'm not sure exactly what you're seeing. Do you mean that when you run leap
on the same inputs, varying only mbondi2 vs mbondi3, that you get different
number of water molecules added to the solute?
On Mon, Oct 21, 2019 at 7:39 AM Rosellen, Martin <
martin.rosellen.16.ucl.ac.uk> wrote:
> Thanks for the recommendation. I just tried to do the MMGBSA calculation
> using my existing trajectories. Unfortunately, using mbondi3 radii instead
> of mbondi2, it seems there are 86 water atoms less when I solvate with
> TIP3P water. As a result I get this error:
>
> Loading and checking parameter files for compatibility...
> mmpbsa_py_energy found! Using
> /s/amber/amber18/CentOS7/amber18/bin/mmpbsa_py_energy
> cpptraj found! Using /s/amber/amber18/CentOS7/amber18/bin/cpptraj
> Preparing trajectories for simulation...
> Error: Number of atoms in NetCDF file (221576) does not match number
> Error: in associated topology (221318)!
> Error: Could not set up '../all_prod_short_samples.nc' for reading.
> Error: Could not set up input trajectory '../all_prod_short_samples.nc'.
> Error: Error(s) occurred during execution.
> File "/s/amber/amber18/CentOS7/amber18/bin/MMPBSA.py.MPI", line 99, in
> <module>
> app.file_setup()
> File
> "/s/amber/amber18/CentOS7/amber18/lib/python2.7/site-packages/MMPBSA_mods/main.py",
> line 156, in file_setup
> self.mpi_size, str(external_progs['cpptraj']), self.pre)
> File
> "/s/amber/amber18/CentOS7/amber18/lib/python2.7/site-packages/MMPBSA_mods/make_trajs.py",
> line 59, in make_trajectories
> traj = Trajectory(FILES.solvated_prmtop, FILES.mdcrd, cpptraj)
> File
> "/s/amber/amber18/CentOS7/amber18/lib/python2.7/site-packages/MMPBSA_mods/make_trajs.py",
> line 467, in __init__
> self.Query()
> File
> "/s/amber/amber18/CentOS7/amber18/lib/python2.7/site-packages/MMPBSA_mods/make_trajs.py",
> line 602, in Query
> raise TrajError('%s failed when querying %s' % (self.exe, traj))
> TrajError: /s/amber/amber18/CentOS7/amber18/bin/cpptraj failed when
> querying ../all_prod_short_samples.nc
> Error occured on rank 0.
> Exiting. All files have been retained.
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> with errorcode 1.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> --------------------------------------------------------------------------
>
> Is there any way I could use existing trajectories for MMGBSA calculations
> switching form mbondi2 to mbondi3?
>
> cheers
> Martin
>
> Message: 18
> Date: Thu, 10 Oct 2019 14:06:05 -0400
> From: Carlos Simmerling <carlos.simmerling.gmail.com<mailto:
> carlos.simmerling.gmail.com>>
> Subject: Re: [AMBER] Calculate MMGBSA keeping water in binding site
> To: AMBER Mailing List <amber.ambermd.org<mailto:amber.ambermd.org>>
> Message-ID:
> <CAGk3s-Rku-KXHJbroDAvfGPnnvqxM=vEh5NqRjd0BdqQvaNq0w.mail.gmail.com
> <mailto:CAGk3s-Rku-KXHJbroDAvfGPnnvqxM=vEh5NqRjd0BdqQvaNq0w.mail.gmail.com
> >>
> Content-Type: text/plain; charset="UTF-8"
>
> we have a few papers looking at performance of GB vs explicit water for
> salt bridges (see below). I don't recall testing igb=2, but the others tend
> to overestimate strength, especially with mbondi2. We recommend mbondi3
> along with igb=8, see the Nguyen et al paper below for analysis.
> carlos
>
> Improved Generalized Born Solvent Model Parameters for Protein Simulations
> Nguyen, H., Roe, D. R., Simmerling, C., Journal of Chemical Theory and
> Computation, 2013, 9 (4), 2020-2034
> DOI: 10.1021/ct3010485
> PMCID: PMC4361090
>
> Improving the description of salt bridge strength and geometry in a
> Generalized Born model
> Shang, Y., Nguyen, H., Wickstrom, L., Okur, A. and Simmerling, C., Journal
> of Molecular Graphics and Modelling., 2011, 29, 676-684
> DOI: 10.1016/j.jmgm.2010.11.013
> PMCID: PMC3390179
>
> Evaluation of salt bridge structure and energetics in peptides using
> explicit, implicit and hybrid solvation models
> Okur, A., Wickstrom, L. and Simmerling, C.
> Journal of Chemical Theory and Computation, 2008, 4 (3), 488-498
> DOI: 10.1021/ct7002308
>
> Investigation of salt bridge stability in a Generalized Born solvent model
> Geney, R., Layten, M., Gomperts, R., Hornak, V. and Simmerling, C.
> Journal of Chemical Theory and Computation, 2006 , 2 (1), 115-127
> DOI: 10.1021/ct050183l
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Received on Mon Oct 21 2019 - 06:00:05 PDT
