Re: [AMBER] examination of ligand binding energy as a function of simulation time with MMPBSA calculations

From: Ray Luo <rluo.uci.edu> Date: Sun, 12 Apr 2020 19:33:47 -0700

--
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 Sat, Apr 11, 2020 at 7:49 AM Billiot, Eugene
<Eugene.Billiot.tamucc.edu> wrote:
>
> Hello All,
> I am using MMPBSA to calculate ligand binding energies for a variety of analytes with various amino acid based micellar systems.  I would like to be able to plot ligand binding energy as a function of simulation time.  When running MMPBSA calculations does it calculate energies for each frame and then print out an average at the end.  If so, does it create a file with the calculated PG and GB energies per frame that I can then use to plot energy calculations for each frame?  Is there any way I can examine the binding energy as a function of simulation time?
>
> ________________________________
> From: David A Case <david.case.rutgers.edu>
> Sent: Saturday, April 11, 2020 7:03 AM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Amber18 compiled with GCC/8.3.0 fails some DPFP tests
>
> On Fri, Apr 10, 2020, Cong Liu wrote:
> >
> >I recently compiled Amebr18 with GCC/8.3.0 and CUDA/10.1. The compilation
> >went through well. However, *amber_cuda_serial *testing indicates 5 "*file
> >comparison failure*":  DPFP myoglobin_igb7, DPFP myoglobin_igb8, DPFP
> >myoglobin_igb8_gbsa, DPFP irest1_ntt0_igb7_ntc2, DPFP irest1_ntt0_igb8_ntc2
> >with "IEEE_UNDERFLOW_FLAG IEEE_DENORMAL" floating-point exceptions.
>
> The underflow flag is not worrisome, but you should look at the .dif
> files (collected in the logs folder) and see if the discrepancies look
> like roundoff errors or something more serious.
>
> ....dac
>
>
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