Re: [AMBER] MMPBSA runs GB but fails in PB for RNA-ligand complex

From: Kasprzak, Wojciech (NIH/NCI) [C] <"Kasprzak,>
Date: Wed, 11 Apr 2018 19:47:02 +0000

Dr. Luo,

Thank you very much! Indeed, I now have a run under way with radiopt=0.

I would still like to understand if there are any potential problems with using
PME-based trajectory with, say mbondi2 or mbondi parameters in the topology file
with a follow-up MMPBSA PB calculations for which the Amber manual
recommends bondi parameters.

Also, in principle, if I have a trajectory based on explicit solvent run, but with only
the RNA & ligand atoms saved, will the MMPBSA calculation run with the solvent-free
topology file used twice for the -sp and -cp parameters?

Thank you again, and I would appreciate some clarification of the remaining
two questions.

Best regards,, Voytek

Wojciech (Voytek) Kasprzak (Contractor)
Analyst Programmer
Frederick National Laboratory for Cancer Research
Leidos Biomedical Research, Inc.
Post Office Box B
Frederick, Maryland 21702
Phone: 301-846-5537
kasprzaw.mail.nih.gov
http://binkley2.ncifcrf.gov/users/kasprzak

________________________________________
From: Ray Luo [rluo.uci.edu]
Sent: Wednesday, April 11, 2018 12:46 PM
To: AMBER Mailing List
Subject: Re: [AMBER] MMPBSA runs GB but fails in PB for RNA-ligand complex

Voytek,

Set radiopt=0 to use the radii in the prmtop file should resolve this issue.

Ray
--
Ray Luo, Ph.D.
Professor of Structural Biology/Biochemistry/Biophysics,
Chemical Physics, Biomedical Engineering, and Chemical Engineering
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
On Wed, Apr 11, 2018 at 7:47 AM, Kasprzak, Wojciech (NIH/NCI) [C]
<wojciech.kasprzak.nih.gov> wrote:
>   Dear Amber Users,
>
> This is Voytek Kasprzak from Frederick National Lab (NCI).  I am unable to complete a simple
> MMPBSA run based on Amber Advanced Tutorial 3 (section 3.4) in Amber 16 or Amber 14.
> My case is similar but not the same as a post on the PB failure from yesterday.
>
> I am analyzing a trajectory of an RNA fragment with a small ligand (~60 atoms), that was
> subjected to explicit solvent PME MD simulation in Amber 16.  All topology files
> (complex in solvent, complex without solvent, receptor alone and ligand alone) were created
> in one LEaP session with the same PBRadii - a potential issue, as the end of the FILE.o*
> shown below seems to suggest (see 1. below)
>
> After completing successfully the GB-based section of the MMPBSA.py.MPI run (10,000 input
> frames on 16 cores), the program crashes reproducibly as it gets to the PB-based calculations.
> The error message states that "No radius assigned for atom     3  C5'   CI" is the problem,
> and one PB output file _MMPBSA_complex_pb.mdout.2 shows an aborted start of that section
> (see 2. below).  C5' is the third atom in the RNA/lifand prmtop file (oddly, no complaints
> about the first two atoms: HO5' and O5'). The input file is shown in point 3.
>
> Should I create separate no-solvent topology files with PBRadii set to bondi since that is
> the common denominator for igb=2 and pbsa runs?  What would you recommend for RNA/DNA-ligand
> complexes? What are the consequences of having solvent run based on one set of radii and
> solvent-free parts on another?
> If my interpretation of the error messages is incorrect, what else could be the problem?
>
> Best regards,  Voytek
>
> Wojciech (Voytek) Kasprzak (Contractor)
> Analyst Programmer
> Frederick National Laboratory for Cancer Research
> Leidos Biomedical Research, Inc.
> Post Office Box B
> Frederick, Maryland 21702
> Phone: 301-846-5537
> kasprzaw.mail.nih.gov
> http://binkley2.ncifcrf.gov/users/kasprzak
>
> ==================================================================
> 1. Error message:
>
>   File "/opt/nasapps/production/amber/amber16/bin/MMPBSA.py.MPI", line 100, in <module>
>     app.run_mmpbsa()
>   File "/opt/nasapps/production/amber/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 218, in run_mmpbsa
>     self.calc_list.run(rank, self.stdout)
>   File "/opt/nasapps/production/amber/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 82, in run
>     calc.run(rank, stdout=stdout, stderr=stderr)
>   File "/opt/nasapps/production/amber/amber16/lib/python2.7/site-packages/MMPBSA_mods/calculation.py", line 433, in run
>     self.prmtop) + '\n\t'.join(error_list) + '\n')
> CalcError: /opt/nasapps/production/amber/amber16/bin/mmpbsa_py_energy failed with prmtop RNA-LIGAND-nosolv.prmtop!
>         PB Bomb in pb_aaradi(): No radius assigned for atom     3  C5'   CI
>
> Error occured on rank 2.
> Exiting. All files have been retained.
>
>
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Received on Wed Apr 11 2018 - 13:00:02 PDT
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