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Valdes-Tresanco-MS / gmx_MMPBSA

gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.
https://valdes-tresanco-ms.github.io/gmx_MMPBSA/
GNU General Public License v3.0
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[Bug-gmx_MMPBSA]: gmx_MMPBSA does not support water/ions molecules in any structure #501

Open Howpow88 opened 2 months ago

Howpow88 commented 2 months ago

Bug summary

i havn't used this in a while and i have the following error: gmx_MMPBSA does not support water/ions molecules in any structure, but we found 127 molecules in the complex. any idea how to fix this? last time i ran i don't remember removing all the waters

Terminal output

here is the commdand i put in the terminal:

gmx_MMPBSA -O -i mmpbsa.in -cs md_0_1.tpr -ct md_0_2.xtc -ci indexfile.ndx -cg 15 16 -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

gmx_MMPBSA.log

gmx_MMPBSA.log

Operating system

linux

gmx_MMPBSA Version

gmx_MMPBSA

Python version

3.9

Installation

conda AmberTools + conda

marioernestovaldes commented 2 months ago

Usually happens when there is some name similar to those of ions in the force fields. could you please share the files you are using?