Problem with polar solvation energy calculations

[Dovydas Vasiliauskas]

Hello,

I am a new user of g_mmpbsa. The pre-compiled g_mmpbsa executable with included gromacs-5.1 and apbs functionality worked properly for the 1EBZ tutorials. However, I get errors when I run polar solvation energy calculations for a bigger protein-membrane system.

For my polar solvation energy calculations, I am using the script "g_mmpbsa -f traj.trr -s production.tpr -n index.ndx -i polar.mdp -nomme -pbsa -decomp". After several rounds of PBE calculations running I get an error:

Parsed input file.
Got paths for 1 molecules
Reading PQR-format atom data from pSmp1tgA.pqr.
Vio_ctor2: Gethostbyname fail INET sock <> dueto <ENOENT>
  95220 atoms
  Centered at (7.350e+01, 7.368e+01, 1.076e+02)
  Net charge -2.01e+02 e
NOsh_setupCalcMGPARA:  Oops!  You're trying to perform an 'mg-para' (parallel) calculation
NOsh_setupCalcMGPARA:  with a version of APBS that wasn't compiled with MPI!
NOsh_setupCalcMGPARA:  Perhaps you meant to use the 'async' flag?
NOsh_setupCalcMGPARA:  Bailing out!
NOsh_setupCalcMGPARA:  Oops!  You're trying to perform an 'mg-para' (parallel) calculation
NOsh_setupCalcMGPARA:  with a version of APBS that wasn't compiled with MPI!
NOsh_setupCalcMGPARA:  Perhaps you meant to use the 'async' flag?
NOsh_setupCalcMGPARA:  Bailing out!
Preparing to run 0 PBE calculations.
----------------------------------------
PRINT STATEMENTS

print energy 1 (mol1) - 2 (mol2) end
Segmentation fault (core dumped)

A similar error has been reported by other g_mmpbsa community members already in 2016. What is different for me is that I followed the provided answer and documentation, and inserted the line mg-type = mg-auto  into polar.mdp file (it was not there originally, I assume mg-type=mg-para is the default), however, I am still getting the same error.

Do you know what could be the problem here and could you please recommend how to fix it?

Thank you very much for your time,

With best wishes,

[Rajendra Kumar]

Hi,

Please increase the value of gmemceil and try again. Currently, mg-type is automatically assigned depending on the memory requirement.

Thanks!

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