search

Valdes-Tresanco-MS / gmx_MMPBSA

gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.
https://valdes-tresanco-ms.github.io/gmx_MMPBSA/
GNU General Public License v3.0
211 stars 64 forks source link

[Bug-gmx_MMPBSA]: gmx_MMPBSA does not support water/ions molecules in any structure, but we found 113 molecules in the complex #483

Open Premanandabasak opened 4 months ago

Premanandabasak commented 4 months ago

Bug summary

Hi! I have been encountering this issue recently with the calculation. I have before hand removed pbc conditions and generated no pbc file for the execution of mmpbsa calculation but I am still getting this error. I have attached the error message below for the reference. Please help me resolve this. ##############################################

[ERROR ] MMPBSA_Error

gmx_MMPBSA does not support water/ions molecules in any structure, but we found 113 molecules in the complex.

Check the gmx_MMPBSA.log file to report the problem. File "/home/premananda/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in sys.exit(gmxmmpbsa()) File "/home/premananda/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa app.make_prmtops() File "/home/premananda/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 681, in make_prmtops self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology() File "/home/premananda/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 122, in buildTopology self.gmx2pdb() File "/home/premananda/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 519, in gmx2pdb self.check4water() File "/home/premananda/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 541, in check4water GMXMMPBSA_ERROR(f'gmx_MMPBSA does not support water/ions molecules in any structure, but we found' File "/home/premananda/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in init raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.') MMPBSA_Error:

gmx_MMPBSA does not support water/ions molecules in any structure, but we found 113 molecules in the complex.

Check the gmx_MMPBSA.log file to report the problem. Exiting. All files have been retained.

Terminal output

[ERROR  ] MMPBSA_Error 

gmx_MMPBSA does not support water/ions molecules in any structure, but we found 113 molecules in the complex.

Check the gmx_MMPBSA.log file to report the problem.
  File "/home/premananda/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/premananda/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa
    app.make_prmtops()
  File "/home/premananda/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 681, in make_prmtops
    self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology()
  File "/home/premananda/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 122, in buildTopology
    self.gmx2pdb()
  File "/home/premananda/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 519, in gmx2pdb
    self.check4water()
  File "/home/premananda/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 541, in check4water
    GMXMMPBSA_ERROR(f'gmx_MMPBSA does not support water/ions molecules in any structure, but we found'
  File "/home/premananda/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
    raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error: 

gmx_MMPBSA does not support water/ions molecules in any structure, but we found 113 molecules in the complex.

Check the gmx_MMPBSA.log file to report the problem.
Exiting. All files have been retained.

gmx_MMPBSA.log

gmx_MMPBSA.log

Operating system

Linux

gmx_MMPBSA Version

gmx_MMPBSA v1.6.3

Python version

Python 3.9.19

Installation

conda AmberTools + conda

Valdes-Tresanco-MS commented 4 months ago

Can you send me the structure file to check them?

Premanandabasak commented 4 months ago

Dear Sir, Please find the attachment.

On Mon, Apr 15, 2024 at 7:40 PM Mario Sergio Valdés Tresanco < @.***> wrote:

Can you send me the structure file to check them?

— Reply to this email directly, view it on GitHub https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/issues/483#issuecomment-2056958346, or unsubscribe https://github.com/notifications/unsubscribe-auth/BH2ZXWMP7TLCTUOYW347NATY5PNXFAVCNFSM6AAAAABGHHI5ICVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANJWHE2TQMZUGY . You are receiving this because you authored the thread.Message ID: @.***>

Premanandabasak commented 4 months ago

Hi! have you looked into the structure file? Please give me the required suggestions to overcome this error.

Valdes-Tresanco-MS commented 4 months ago

@Premanandabasak Can you send me the structures using GitHub directly or through Google Drive, One Drive, or any other system? Please don't reply directly to the email because this method doesn't allow attaching any file.

Premanandabasak commented 4 months ago

Here the attached file complex.zip

Valdes-Tresanco-MS commented 4 months ago

Sorry for the delay. I don't see any problem with the structure. Can you send me the files you are using to reproduce the problem?