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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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[Question]: MMPBSA_Error: Could not find necessary program [sander.APBS] #451

Closed fatih4534 closed 10 months ago

fatih4534 commented 10 months ago

My Question is...

Hi sir, I would like to compute binding energy for my complex using mmpbsa module. However, when I tended to use sander.apbs typing sander_apbs=1 in &pb section, I got an error. How can I fix this error?

marioernestovaldes commented 10 months ago

could you please share the gmx_MMPBSA.log file?

marioernestovaldes commented 10 months ago

oh, I see... we haven't done much testing ion sander.APBS, but it needs to be installed before using it (https://mccammon.ucsd.edu/iapbs/doc/amber.html). Any particular reason to use sander.APBS and not sander to perform the calculation?

On Sun, Jan 7, 2024 at 2:38 PM fatih4534 @.***> wrote:

The log file is in the attachment. gmx_MMPBSA.log https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/files/13854999/gmx_MMPBSA.log

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fatih4534 commented 10 months ago

Indeed, I tend to compare mmpbsa calculations using gmx_MMPBSA to VMD plugin called caFE. Since apbs is used in the vmd plugin, I could not make sure the energy values while comparing.

fatih4534 commented 10 months ago

Thank you for your answer sir :)