I would suggest visualizing your trajectory, especially at the frame that
is giving you the nan error values. That is usually indicative of a
structure irregularly (such as overlapping atoms between a ligand and
receptor).
Hope that helps.
-Bill
On Thu, Apr 6, 2023 at 8:24 AM Abraham, Sarah via AMBER <amber.ambermd.org>
wrote:
> Hi,
>
> I am running MMPBSA simulations with the LRH-1 receptor and a ligand. I
> have made files for the complex of the two, the receptor alone, the ligand.
> I have no problem running the simulation, but then when I get to the
> analysis, I use the analysis script that is on amber tutorials website.
> However, the files run until the _MMPSA_complex_gb.mdout.0 file and within
> the nohup file I have this error:
>
> Beginning GB calculations with /usr/local/amber20/bin/mmpbsa_py_energy
> calculating complex contribution...
> File "/usr/local/amber20/bin/MMPBSA.py", line 100, in <module>
> app.run_mmpbsa()
> File
> "/usr/local/amber20/lib/python3.8/site-packages/MMPBSA_mods/main.py", line
> 218, in run_mmpbsa
> self.calc_list.run(rank, self.stdout)
> File
> "/usr/local/amber20/lib/python3.8/site-packages/MMPBSA_mods/calculation.py",
> line 82, in run
> calc.run(rank, stdout=stdout, stderr=stderr)
> File
> "/usr/local/amber20/lib/python3.8/site-packages/MMPBSA_mods/calculation.py",
> line 156, in run
> raise CalcError('%s failed with prmtop %s!' % (self.program,
> CalcError: /usr/local/amber20/bin/mmpbsa_py_energy failed with prmtop
> com.top!
> Exiting. All files have been retained.
>
>
> Within the _MMPSA_complex_gb.mdout.0 file, I have these errors:
>
> Processing frame 5
> /usr/local/amber20_src/AmberTools/src/sff/eff.c(2675) enb14 --> -nan
> /usr/local/amber20_src/AmberTools/src/sff/eff.c(2676) eel14 --> -nan
> /usr/local/amber20_src/AmberTools/src/sff/eff.c(2734) enb --> -nan
> /usr/local/amber20_src/AmberTools/src/sff/eff.c(2735) eel --> -nan
> /usr/local/amber20_src/AmberTools/src/sff/eff.c(2736) e_gb --> nan
> /usr/local/amber20_src/AmberTools/src/sff/eff.c(2737) esurf --> 0.000
> /usr/local/amber20_src/AmberTools/src/sff/eff.c(2738) evdwnp --> 0.000
> BOND = -nan ANGLE = -nan DIHED =
> -nan
> VDWAALS = -nan EEL = -nan EGB =
> nan
> 1-4 VDW = -nan 1-4 EEL = -nan RESTRAINT =
> 0.0000
> ESURF = 0.0000
>
> Processing frame 6
> /usr/local/amber20_src/AmberTools/src/sff/eff.c(2675) enb14 --> -nan
> /usr/local/amber20_src/AmberTools/src/sff/eff.c(2676) eel14 --> -nan
> /usr/local/amber20_src/AmberTools/src/sff/eff.c(2734) enb --> -nan
> /usr/local/amber20_src/AmberTools/src/sff/eff.c(2735) eel --> -nan
> /usr/local/amber20_src/AmberTools/src/sff/eff.c(2736) e_gb --> nan
> /usr/local/amber20_src/AmberTools/src/sff/eff.c(2737) esurf --> 0.000
> /usr/local/amber20_src/AmberTools/src/sff/eff.c(2738) evdwnp --> 0.000
> BOND = -nan ANGLE = -nan DIHED =
> -nan
> VDWAALS = -nan EEL = -nan EG
>
>
> I have been looking through the amber archives for an answer on how to fix
> this but I have been unable to find an answer.
>
>
> Thank you, and hope to hear from you soon,
>
> Sarah Abraham
>
> Emory 23' Biology B.S | Chemistry B.A
> Student Researcher Ortlund Lab
> Scribe Emory University Hospital
>
>
>
>
> Sarah Abraham
>
> Emory 23' Biology B.S | Chemistry B.A
> Student Researcher Ortlund Lab
> Scribe Emory University Hospital
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Assistant Professor of Chemistry
Truman State University
417-549-0952
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Received on Fri Apr 07 2023 - 17:00:02 PDT
