The binding free energy in molecular dynamics can be obtained from mmpbsa and could be determine the most stable ligand in molecular dynamics simulation. After running production, i try the mmpbsa calculation with the script, but it gave me error like this. So, what should i check first? Any suggestion can help. Thank you
Rajesh Pal
I would check for mismatch in versions as well as system memory.
Refer to this thread:
http://archive.ambermd.org/201611/0119.html
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Martiniano Bello
Hi Saiful, it seems a problem in the definition of your .prmtop files. I suggest you to carefully check your prmtops.
Regards
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Zhaoxi Sun
Some errors in prmtop, memory issue, and various reasons could cause this. I think the prmtop files should be the first one to check, as mentioned by Martiniano.
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