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

From: Rosellen, Martin <>
Date: Fri, 1 Nov 2019 17:24:54 +0000

Yes, exactly.

Giving it some thought, I think it might be best to rerun my simulations using mbondi3 ab initio instead of making ‚mbondi3-calculations' on the base of trajectories that were produced using mbondi2.

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 <<>> 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
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
line 156, in file_setup
   self.mpi_size, str(external_progs['cpptraj']), self.pre)
line 59, in make_trajectories
   traj = Trajectory(FILES.solvated_prmtop, FILES.mdcrd, cpptraj)
line 467, in __init__
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?

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Received on Fri Nov 01 2019 - 10:30:02 PDT
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