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[Miller, Bill R, T Dwight McGee, Jason M Swails, Nadine Homeyer, Holger Gohlke, and Adrian E Roitberg. “MMPBSA.Py : An Efficient Program for End-State Free Energy Calculations.” *Journal of Chemical T…
cramg updated
3 years ago
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[system1.zip](https://github.com/ParmEd/ParmEd/files/5738441/system1.zip)
I used the command :"ante-MMPBSA.py -p system1.prmtop -s ":WAT" --radii mbondi2 -c s-ket_pro.prmtop" to create complex.prmt…
957-z updated
3 years ago
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Hello,
I’d like to ask whether g_mmpbsa is supported on Linux/Mac ARM64 systems ?
Any concerns ?
Any positive/negative experience ?
Thank you!
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Hi,
I have cloned the source code for g_mmpbsa from GitHub but can not find the `configure' shell script to install GMM..?
Please help!
Thanks in advance,
Ash
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The GB computation works fine but for the PB it is stuck at 0 frames and prints the following note in the console:
> Note: The following floating-point exceptions are signalling: IEEE_INVALID_FLAG …
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in g_mmpbsa ,there is not manual of mutate_traj_tpr.py, so we do not kown how to utilize it. can manual of mutate_traj_tpr.py be added?
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Is it possible to use the software for the calculation of energy differences between a WT monomer and a mutated monomer, both of them are not a complex, so I cannot define a ligand and receptor. I hav…
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May I know where to get the builtins module so I can run the calculation for average binding energy?
Traceback (most recent call last):
File "../mmpbsa/MmPbSaStat.py", line 39, in
from bui…
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Dear Dr. Li,
I have used gmx_MMPBSA.bsh to calculate the Gibes free energy. But the last step always reported error which is :awk: cmd. line:468: (FILENAME=_pid.pdb FNR=119376) warning: exp: argumen…
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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!