[Question]: How to calculate GB

[Admire7494]

My Question is...

[INFO ] Starting gmx_MMPBSA v1.6.2 [INFO ] Command-line gmx_MMPBSA -O -i mmpbsa_2b.in -cs md.tpr -ci index.ndx -cg 1 14 -ct md.xtc -cp complex.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv [INFO ] Checking mmpbsa_2b.in input file... [INFO ] Checking mmpbsa_2b.in input file...Done. [INFO ] Checking external programs... [INFO ] cpptraj found! Using /home/wangmuqiang/.conda/envs/gmxMMPBSA/bin/cpptraj [INFO ] tleap found! Using /home/wangmuqiang/.conda/envs/gmxMMPBSA/bin/tleap [INFO ] parmchk2 found! Using /home/wangmuqiang/.conda/envs/gmxMMPBSA/bin/parmchk2 [INFO ] sander found! Using /home/wangmuqiang/.conda/envs/gmxMMPBSA/bin/sander [INFO ] Using GROMACS version > 5.x.x! [INFO ] gmx found! Using /home/wangmuqiang/.conda/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 Protein_NADH (1_14) 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 Protein (1) 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 NADH (14) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb [INFO ] Checking the structures consistency... [INFO ] [INFO ] Using topology conversion. Setting radiopt = 0... [INFO ] Building Normal Complex Amber topology... [INFO ] Detected Amber/OPLS force field topology format... [WARNING] 46 invalid DIHEDRAL_PERIODICITY = 0 found in Complex topology... Setting DIHEDRAL_PERIODICITY = 1 [INFO ] Assigning PBRadii mbondi2 to Complex... [INFO ] Writing Normal Complex AMBER topology... [INFO ] No Receptor topology file was defined. Using ST approach... [INFO ] Building AMBER Receptor topology from Complex... [INFO ] Assigning PBRadii mbondi2 to Receptor... [INFO ] Writing Normal Receptor AMBER topology... [INFO ] No Ligand topology file was defined. Using ST approach... [INFO ] Building AMBER Ligand topology from Complex... [INFO ] Assigning PBRadii mbondi2 to Ligand... [INFO ] Writing Normal Ligand AMBER topology... [INFO ] Cleaning normal complex trajectories... [INFO ] Building AMBER topologies from GROMACS files... Done. [INFO ] Loading and checking parameter files for compatibility... File "/home/wangmuqiang/.conda/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in sys.exit(gmxmmpbsa()) File "/home/wangmuqiang/.conda/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 100, in gmxmmpbsa app.file_setup() File "/home/wangmuqiang/.conda/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 127, in file_setup create_inputs(INPUT, self.normal_system, self.pre) File "/home/wangmuqiang/.conda/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/createinput.py", line 263, in create_inputs gb_mdin.make_mdin() File "/home/wangmuqiang/.conda/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/createinput.py", line 327, in make_mdin self.mdin.change(self.parent_namelist[key], key, value) File "/home/wangmuqiang/.conda/envs/gmxMMPBSA/lib/python3.9/site-packages/parmed/amber/mdin/mdin.py", line 197, in change if (value[0] == value[-1] == "'") or (value[0] == value[-1] == '"'): IndexError: string index out of range Exiting. All files have been retained.

The mmpbsa.in : Input file for running PB and GB in serial &general startframe=1, endframe=4, interval=1, keep_files=2, / &gb igb=5, saltcon=0.100, / &pb istrng=0.100, /

[marioernestovaldes]

did you install Parmed from our repository?

python -m pip install git+https://github.com/Valdes-Tresanco-MS/ParmEd.git@v3.4

[Admire7494]

It's difficult to run this command. So i download the ParmEd to the anaconda environment and run command "python -m pip install . -U". The ParmEd was downloaded by bilibili

[Admire7494]

_libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge ambertools 21.12 py39hc630cb1_0 conda-forge amberutils 21.0 pypi_0 pypi arpack 3.7.0 hdefa2d7_2 conda-forge binutils 2.39 hdd6e379_1 conda-forge binutils_impl_linux-64 2.39 he00db2b_1 conda-forge binutils_linux-64 2.39 h5fc0e48_13 conda-forge boost-cpp 1.74.0 h75c5d50_8 conda-forge brotli 1.1.0 hd590300_1 conda-forge brotli-bin 1.1.0 hd590300_1 conda-forge bzip2 1.0.8 hd590300_5 conda-forge c-ares 1.24.0 hd590300_0 conda-forge c-compiler 1.2.0 h7f98852_0 conda-forge ca-certificates 2023.11.17 hbcca054_0 conda-forge certifi 2023.11.17 pyhd8ed1ab_0 conda-forge compilers 1.2.0 ha770c72_0 conda-forge contourpy 1.2.0 py39h7633fee_0 conda-forge curl 7.87.0 h6312ad2_0 conda-forge cxx-compiler 1.2.0 h4bd325d_0 conda-forge cycler 0.12.1 pyhd8ed1ab_0 conda-forge cython 3.0.7 py39h3d6467e_0 conda-forge expat 2.5.0 hcb278e6_1 conda-forge fftw 3.3.10 nompi_hc118613_108 conda-forge fonttools 4.47.0 py39hd1e30aa_0 conda-forge fortran-compiler 1.2.0 h1990efc_0 conda-forge freetype 2.12.1 h267a509_2 conda-forge gcc_impl_linux-64 9.5.0 h99780fb_19 conda-forge gcc_linux-64 9.5.0 h4258300_13 conda-forge gettext 0.21.1 h27087fc_0 conda-forge gfortran_impl_linux-64 9.5.0 hf1096a2_19 conda-forge gfortran_linux-64 9.5.0 hdb51d14_13 conda-forge git 2.39.1 pl5321ha3eba64_0 conda-forge gmx-mmpbsa 1.6.2 pypi_0 pypi gromacs 2022.4 nompi_hca75aac_100 conda-forge gxx_impl_linux-64 9.5.0 h99780fb_19 conda-forge gxx_linux-64 9.5.0 h43f449f_13 conda-forge hdf4 4.2.15 h9772cbc_5 conda-forge hdf5 1.12.2 nompi_h2386368_101 conda-forge icu 70.1 h27087fc_0 conda-forge importlib-resources 6.1.1 pyhd8ed1ab_0 conda-forge importlib_resources 6.1.1 pyhd8ed1ab_0 conda-forge jpeg 9e h0b41bf4_3 conda-forge kernel-headers_linux-64 2.6.32 he073ed8_16 conda-forge keyutils 1.6.1 h166bdaf_0 conda-forge kiwisolver 1.4.5 py39h7633fee_1 conda-forge krb5 1.20.1 hf9c8cef_0 conda-forge lcms2 2.15 hfd0df8a_0 conda-forge ld_impl_linux-64 2.39 hcc3a1bd_1 conda-forge lerc 4.0.0 h27087fc_0 conda-forge libaec 1.1.2 h59595ed_1 conda-forge libblas 3.9.0 20_linux64_openblas conda-forge libbrotlicommon 1.1.0 hd590300_1 conda-forge libbrotlidec 1.1.0 hd590300_1 conda-forge libbrotlienc 1.1.0 hd590300_1 conda-forge libcblas 3.9.0 20_linux64_openblas conda-forge libcurl 7.87.0 h6312ad2_0 conda-forge libdeflate 1.17 h0b41bf4_0 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 hd590300_2 conda-forge libexpat 2.5.0 hcb278e6_1 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libgcc-devel_linux-64 9.5.0 h0a57e50_19 conda-forge libgcc-ng 13.2.0 h807b86a_3 conda-forge libgfortran-ng 13.2.0 h69a702a_3 conda-forge libgfortran5 13.2.0 ha4646dd_3 conda-forge libgomp 13.2.0 h807b86a_3 conda-forge libhwloc 2.9.0 hd6dc26d_0 conda-forge libiconv 1.17 hd590300_2 conda-forge liblapack 3.9.0 20_linux64_openblas conda-forge libnetcdf 4.8.1 nompi_h261ec11_106 conda-forge libnghttp2 1.51.0 hdcd2b5c_0 conda-forge libnsl 2.0.1 hd590300_0 conda-forge libopenblas 0.3.25 pthreads_h413a1c8_0 conda-forge libpng 1.6.39 h753d276_0 conda-forge libsanitizer 9.5.0 h2f262e1_19 conda-forge libsqlite 3.44.2 h2797004_0 conda-forge libssh2 1.10.0 haa6b8db_3 conda-forge libstdcxx-devel_linux-64 9.5.0 h0a57e50_19 conda-forge libstdcxx-ng 13.2.0 h7e041cc_3 conda-forge libtiff 4.5.0 h6adf6a1_2 conda-forge libuuid 2.38.1 h0b41bf4_0 conda-forge libwebp-base 1.3.2 hd590300_0 conda-forge libxcb 1.13 h7f98852_1004 conda-forge libxcrypt 4.4.36 hd590300_1 conda-forge libxml2 2.10.3 hca2bb57_4 conda-forge libzip 1.9.2 hc869a4a_1 conda-forge libzlib 1.2.13 hd590300_5 conda-forge matplotlib-base 3.8.2 py39he9076e7_0 conda-forge mpi 1.0 mpich conda-forge mpi4py 3.1.3 py39h32b9844_3 conda-forge mpich 4.1.2 h846660c_101 conda-forge munkres 1.1.4 pyh9f0ad1d_0 conda-forge ncurses 6.4 h59595ed_2 conda-forge netcdf-fortran 4.5.4 nompi_hc402ea5_102 conda-forge numpy 1.26.3 py39h474f0d3_0 conda-forge ocl-icd 2.3.1 h7f98852_0 conda-forge openjpeg 2.5.0 hfec8fc6_2 conda-forge openmpi 0.0.1 pypi_0 pypi openssl 1.1.1w hd590300_0 conda-forge packaging 23.2 pyhd8ed1ab_0 conda-forge packmol 20.010 h86c2bf4_0 conda-forge packmol-memgen 1.2.1rc0 pypi_0 pypi pandas 1.2.2 pypi_0 pypi parmed 0+unknown pypi_0 pypi pcre2 10.40 hc3806b6_0 conda-forge perl 5.32.1 7_hd590300_perl5 conda-forge pillow 9.4.0 py39h2320bf1_1 conda-forge pip 23.3.2 pyhd8ed1ab_0 conda-forge pthread-stubs 0.4 h36c2ea0_1001 conda-forge pyparsing 3.1.1 pyhd8ed1ab_0 conda-forge pyqt5 5.15.6 pypi_0 pypi pyqt5-qt5 5.15.2 pypi_0 pypi pyqt5-sip 12.13.0 pypi_0 pypi python 3.9.15 h47a2c10_0_cpython conda-forge python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge python-tzdata 2023.4 pyhd8ed1ab_0 conda-forge python_abi 3.9 4_cp39 conda-forge pytraj 2.0.6 pypi_0 pypi pytz 2023.3.post1 pyhd8ed1ab_0 conda-forge readline 8.2 h8228510_1 conda-forge sander 16.0 pypi_0 pypi scipy 1.11.4 py39h474f0d3_0 conda-forge seaborn 0.11.2 pypi_0 pypi setuptools 69.0.3 pyhd8ed1ab_0 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge sysroot_linux-64 2.12 he073ed8_16 conda-forge tk 8.6.13 noxft_h4845f30_101 conda-forge tqdm 4.66.1 pypi_0 pypi tzdata 2023d h0c530f3_0 conda-forge unicodedata2 15.1.0 py39hd1e30aa_0 conda-forge wheel 0.42.0 pyhd8ed1ab_0 conda-forge xorg-kbproto 1.0.7 h7f98852_1002 conda-forge xorg-libice 1.0.10 h7f98852_0 conda-forge xorg-libsm 1.2.3 hd9c2040_1000 conda-forge xorg-libx11 1.8.4 h0b41bf4_0 conda-forge xorg-libxau 1.0.11 hd590300_0 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge xorg-libxext 1.3.4 h0b41bf4_2 conda-forge xorg-libxt 1.3.0 hd590300_0 conda-forge xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge xorg-xproto 7.0.31 h7f98852_1007 conda-forge xz 5.2.6 h166bdaf_0 conda-forge zipp 3.17.0 pyhd8ed1ab_0 conda-forge zlib 1.2.13 hd590300_5 conda-forge zstd 1.5.5 hfc55251_0 conda-forge This is the package in the environment

[Valdes-Tresanco-MS]

Please try the new version, which has several recent dependencies including parmed