Re: [AMBER] Calculate MMGBSA keeping water in binding site

From: Rosellen, Martin <>
Date: Mon, 21 Oct 2019 11:39:17 +0000

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 '../' for reading.
Error: Could not set up input trajectory '../'.
Error: Error(s) occurred during execution.
  File "/s/amber/amber18/CentOS7/amber18/bin/", line 99, in <module>
  File "/s/amber/amber18/CentOS7/amber18/lib/python2.7/site-packages/MMPBSA_mods/", 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/", 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/", line 467, in __init__
  File "/s/amber/amber18/CentOS7/amber18/lib/python2.7/site-packages/MMPBSA_mods/", 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 ../
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?


Message: 18
Date: Thu, 10 Oct 2019 14:06:05 -0400
From: Carlos Simmerling <<>>
Subject: Re: [AMBER] Calculate MMGBSA keeping water in binding site
To: AMBER Mailing List <<>>
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.

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 - 05:00:01 PDT
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