[AMBER] Warning in MMPBSA calculation with glycoprotein

From: 王 霂生 via AMBER <amber.ambermd.org>
Date: Fri, 10 Feb 2023 18:03:16 +0800

Dear amber users,

I am writing to seek help regarding MMPBSA.py calculations on a glycoprotein system that I am studying. Any insight would be really helpful.

I used MMPBSA.py to calculate the binding energy of a glycoprotein and another protein. The result shows that DIHED contribution has not been canceled completely, which should be zero under normal condition. Such a warning “WARNING: INCONSISTENCIES EXIST WITHIN INTERNAL POTENTIAL TERMS. THE VALIDITY OF THESE RESULTS ARE HIGHLY QUESTIONABLE” appears in the result file.

Then I removed the glycan, used the same parameter to run MD simulation and calculate the binding energy again. Such warning disappeared and the DIHED contribution turned to zero.

The output files are attached. Is there any special parameter that needs to be modified when calculating binding energy with glycan by MMPBSA.py? What mistake I am making ?

Thanks and regards,
Musheng Wang

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Received on Fri Feb 10 2023 - 02:30:02 PST
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