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quantaosun / Ambertools-OpenMM-MD

Open Source, Mostly just clicking mouse to finish a simulation with Ambertools and OpenMM. It was designed to use locally but another notebook to finish the simulaiton on Colab was attached as well.
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Could not find prot_lig_prod_all.dcd #3

Closed pharm-dacnhan closed 1 year ago

pharm-dacnhan commented 1 year ago

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.file_setup() File "/usr/local/lib/python3.10/site-packages/MMPBSA_mods/main.py", line 161, in file_setup self.numframes, self.numframes_nmode = make_trajectories(INPUT, FILES, File "/usr/local/lib/python3.10/site-packages/MMPBSA_mods/make_trajs.py", line 59, in make_trajectories traj = Trajectory(FILES.solvated_prmtop, FILES.mdcrd, cpptraj) File "/usr/local/lib/python3.10/site-packages/MMPBSA_mods/make_trajs.py", line 506, in init self.Query() File "/usr/local/lib/python3.10/site-packages/MMPBSA_mods/make_trajs.py", line 641, in Query raise TrajError('%s failed when querying %s' % (self.exe, traj)) TrajError: /usr/local/bin/cpptraj failed when querying prot_lig_prod_all.dcd

pharm-dacnhan commented 1 year ago

This is my mmpbsa.in content

f = open("mmpbsa.in", "w") f.write("""&general """ + "\n" """ endframe=""" + str(int(1000)) + """, interval=""" + str(int(100)) + """, strip_mask=:WAT:Na+:Cl-:Mg+:K+, """ + "\n" """/ """ + "\n"

MMGBSA calculation

"""&gb """ + "\n" """ igb=""" + str(5) + """, saltcon=""" + str(0.150) + """, """ + "\n" """/ """ + "\n"

MMPBSA CALCULATION

"""&pb """ + "\n" """ istrng=""" + str(0.150) + """, inp=2, radiopt=0, prbrad=1.4, """ + "\n" """/""") f.close()

quantaosun commented 1 year ago

Hi,

I probably have written it in more detail, the mmpbsa code in my notebook is never expected to be used directly since I assume most of my readers already have been familiar with Amber. That is in the parameterisation steps, better to generate all prmtop files for receptor, ligand, etc, or later you could also extract from complex.prmtop. That is something I have not but probably should included in the notebook.

In my notebook, the final trajectory name is trajectory.dcd. Also, you are supposed to change the number of frames used in mmpbsa based actual number of frames in your trajectory file. These are all very basic things people would look at.

I should assure you that a simple MMPBSA or MMGBSA is not hard at all if you don't try to do energy decomposition or other things like Alaine scanning etc. So please just read Amber's manual probably is more efficient than posting here. I will update the notebook eventually but this is not a priority for now. Cheers.

In a general sense about these issues you have raised recently, I would suggest

1- use pablo-arantes if your goal is just to finish some job, it is probably the easiest way to do it.

2- Use gmx_MMPBSA https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/ , if you just want to finish a job and want nice figures and images of mmpbsa analysis.

But if your goal is to develop some script for your project, and you have to use Amber, then probably you have to read Amber's MMPBSA manual quite carefully.