[AMBER] Error in MMPBSA calculation

From: Sruthi Sudhakar <sruthisudhakarraji.gmail.com>
Date: Sat, 15 Jan 2022 03:24:15 +0530

Dear all,

I am trying to do MMPBSA calculation on a trajectory with 2:1 binding of
ligands on a receptor. I want to get the energy calculations for all 2
ligands separately and the system with ligands together. To do this, I have
done the following strategy:
1. Created 2 different nc files from the final production.nc by stripping
out 1 ligand each
2. Generated the corresponding prmtop files by stripping atoms using
ante-MMPBSA.py (for dry complex)

But upon running mmpbsa in this system, the following error popped up.

*Preparing trajectories for simulation...
*Error: In _MMPBSA_complex.mdcrd.0, expect only 3 or 6 box coords, got 4
* Error: Box line=[ 25.896 13.299 29.595 26.322

                  Error: Could not set up '_MMPBSA_complex.mdcrd.0' for
reading. Error:
Could not set up input trajectory '_MMPBSA_complex.mdcrd.0'.
                                      Error: Error(s) occurred during
execution. *

Is it an issue in the generation of files for the purpose of my study? or
could there be any other issue?

The input is :




And the command line:
    MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSAall.dat -sp
complex.prmtop -cp complexdry.prmtop -rp rec.prmtop -lp ligand.prmtop -y

Sruthi Sudhakar
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Received on Fri Jan 14 2022 - 14:00:02 PST
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