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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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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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### Bug summary
For this project I have used the program for around ~8 compounds, three replicates for each compound, everything is fine except for one compound.
But I don't know why it is impossib…
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### Bug summary
when trying to plot the timeseries of dH or -TdS the program quits unexpectedly with pandas error `pandas._config.config.OptionError: "No such keys(s): 'mode.use_inf_as_null'" `
###…
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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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Running tutorial files
energy2bfac -s 1EBZ_pbc_corrected.tpr -i energyMapIn.dat
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Program: energy2bfac, VERSION 5.1.2
Sourc…
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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!
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I get a memory allocation error when .tpr file is coming from a simulation run using gromacs-2019.x
Reading file step7.tpr, VERSION 2019.4 (single precision)
Reading file step7.tpr, VERSION 2019.4 (…
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Dear all,
I was trying to convert a .top and .gro file from Gromacs to Amber .prmtop by using parmed in order to then run MMPBSA calculation.
the complex.prmtop, rec.prmtop, lig.prmtop were generate…
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I executed the command mentioned in the tutorial:
`unigbsa-pipeline -i example/1ceb/1ceb_protein.pdb -l example/1ceb/1ceb_ligand.sdf -o BindingEnergy.csv`
However, I got an error during the executio…