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Hello Lin WANG and Hao Yang,
I am struggling making AutoMD to work with our installation of Schrodinger. Are you able to assist me in successfully installing it ?
kind regards,
Niki
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### Bug summary
Conducting MMPBSA calculations fails on COM.prmtop for some reason. MMGBSA proceeds to completion without issue. Looking in the _GMX_complex_pb.out it seems there's something off wi…
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I found your code is used for running MMPBSA with openMM.
Please help me to run MMGBSA. Thank you very much.
https://github.com/quantaosun/Ambertools-OpenMM-MD/blob/main/Ambertools-OpenMM-MD_GB…
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### My Question is...
gmx_mmpbsa -O -i MMGBSA.in -cs ../md_100.tpr -ct ../md_100.xtc -ci ../index.ndx -cg 3 4 -cp ../topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv WARNING: No ICD…
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I found that there is no option to run MMGBSA in [this code](https://github.com/pablo-arantes/making-it-rain/blob/main/Protein_ligand.ipynb).
Please help me to fix it. Thank you very much.
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### Comment:
Hi,
I am trying to calculate MMPBSA and MMGBSA by using Ambertools and OpenMM in Google colab [from this notebook](https://github.com/quantaosun/Ambertools-OpenMM-MD/blob/682d775f1…
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In the final step, I faced with the following error, can you help me figure out my problem?
Error: Error(s) occurred during execution.
File "/usr/local/bin/MMPBSA.py", line 99, in
app.fil…
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Hii
I was installing gmx_mmpbsa and ran into this problem.
Kindly help.
sudo pip3 install gmx-MMPBSA
WARNING: pip is being invoked by an old script wrapper. This will fail in a future version …
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I was wondering if there any code or package available to calculate binding free energy of a ligand employing alchemical free energy calculation method or MM/PBSA method? There are many MD builds avai…
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### My Question is...
When I use the MMGBSA calculation, the protein pocket contains two small molecules, hem and my ligand. I want to think of hem as part of the protein to calculate the binding ene…