Closed debanjansen48 closed 1 year ago
same error i got if you got a solution, kindly also help me
Please, use the issue template and attach all required info to identify what's going on
sorry for late reply. Thanks for kind consideration
On Thu, Aug 10, 2023 at 11:12 PM Mario Sergio Valdés Tresanco < @.***> wrote:
Closed #398 https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/issues/398 as completed.
— Reply to this email directly, view it on GitHub https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA/issues/398#event-10062194044, or unsubscribe https://github.com/notifications/unsubscribe-auth/AOJ7Q4XEZX75K7HXL6VVSHDXUUMRJANCNFSM6AAAAAA22X6DB4 . You are receiving this because you authored the thread.Message ID: @.*** com>
i got same error please tell me how to solve it
My Question is...
gmx_mmpbsa -O -i MMGBSA.in -cs ../md_100.tpr -ct ../md_100.xtc -ci ../index.ndx -cg 3 4 -cp ../topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv WARNING: No ICDs were found. Either, - Install a conda package providing a OpenCL implementation (pocl, oclgrind, intel-compute-runtime, beignet) or - Make your system-wide implementation visible by installing ocl-icd-system conda package. [INFO ] Starting gmx_MMPBSA v1.6.1 [INFO ] Command-line gmx_MMPBSA -O -i MMGBSA.in -cs ../md_100.tpr -ct ../md_100.xtc -ci ../index.ndx -cg 3 4 -cp ../topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv tets [INFO ] Checking MMGBSA.in input file... [INFO ] Checking MMGBSA.in input file...Done. [INFO ] Checking external programs... [INFO ] cpptraj found! Using /home/debanjan/miniconda3/envs/gmxMMPBSA/bin/cpptraj [INFO ] tleap found! Using /home/debanjan/miniconda3/envs/gmxMMPBSA/bin/tleap [INFO ] parmchk2 found! Using /home/debanjan/miniconda3/envs/gmxMMPBSA/bin/parmchk2 [INFO ] sander found! Using /home/debanjan/miniconda3/envs/gmxMMPBSA/bin/sander [INFO ] Using GROMACS version > 5.x.x! [INFO ] gmx found! Using /home/debanjan/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx [INFO ] Checking external programs...Done. [INFO ] Building AMBER topologies from GROMACS files... [INFO ] Get PDB files from GROMACS structures files... [INFO ] Making gmx_MMPBSA index for complex... [INFO ] Normal Complex: Saving group C-alpha_Backbone (3_4) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb [INFO ] No receptor structure file was defined. Using ST approach... [INFO ] Using receptor structure from complex to generate AMBER topology [INFO ] Normal Receptor: Saving group C-alpha (3) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb [INFO ] No ligand structure file was defined. Using ST approach... [INFO ] Using ligand structure from complex to generate AMBER topology [INFO ] Normal Ligand: Saving group Backbone (4) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb File "/home/debanjan/miniconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in sys.exit(gmxmmpbsa()) File "/home/debanjan/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 98, in gmxmmpbsa app.make_prmtops() File "/home/debanjan/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 687, in make_prmtops self.FILES.mutant_receptor_prmtop, self.FILES.mutant_ligand_prmtop) = maketop.buildTopology() File "/home/debanjan/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 123, in buildTopology self.gmx2pdb() File "/home/debanjan/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/make_top.py", line 492, in gmx2pdb self.resi, self.resl, self.orderl = res2map(self.indexes, self.complex_str) File "/home/debanjan/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/utils.py", line 601, in res2map for e in value['num']: TypeError: string indices must be integers Exiting. All files have been retained.