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dptech-corp / Uni-GBSA

An automatic workflow to perform MM/GB(PB)SA calculations from force field building, and structure optimization to free energy calculation.
Apache License 2.0
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The '-dec' parameter is missing in unigbsa-traj #42

Open CNDOTA opened 11 months ago

CNDOTA commented 11 months ago

If I add '-dec' to decompose energy when using unigbsa-traj, the following error will be raised:

unigbsa-traj: error: unrecognized arguments: -dec

Could you fix this?

Thank you very much!

CNDOTA commented 11 months ago

After looking into the source code, I fix it with -m 'gb,decomposition' and it seems to work.

But I meet another error:

" [INFO ] Writing Normal Ligand AMBER topology... [WARNING] Number of decomp residues to print using print_res = 'within 6' < 2 [INFO ] Increasing cutoff value by 0.1 until number of decomp residues to print >= 2 [ERROR ] MMPBSA_Error

The maximum number of iterations to select interaction residues was reached. Please set print_res with a valid selection.

Check the gmx_MMPBSA.log file to report the problem. "

How could I revise it to perform the decomposition of the residue energy with Uni-GBSA command?

Thank you very much!

Aunity commented 11 months ago

Could you provide more information? Some example of your input files.