gmx-MMPBSA — error while loading shared libraries: libgfortran.so.3: cannot open shared object file
2024-05-11 22:41:01
操作系统Centos8
运行gmx_MMPBSA时，出现error while loading shared libraries: libgfortran.so.3: cannot open shared object file错误：
[userrr@localhost gmx_MMPBSA]$ gmx_MMPBSA -O -i mmpbsa.in -cs md.tpr -ci index.ndx -cg 1 14 -ct fbd.xtc -lm UNK_bcc_gaff.mol2
[INFO ] Starting
[INFO ] Command-linegmx_MMPBSA -O -i mmpbsa.in -cs md.tpr -ci index.ndx -cg 1 14 -ct fbd.xtc -lm UNK_bcc_gaff.mol2[WARNING] protein_forcefield and ligand_forcefield variables are deprecate since version 1.4.1 and will be remove in the next version. Please, use forcefield instead.
[WARNING] entropy variable is deprecate since version 1.4.2 and will be remove in v1.5.0. Please, use qh_entropy for Quasi-Harmonic approximation and i_entropy for Interaction entropy approximation instead.
[WARNING] entropy_seg variable is deprecate since version 1.4.2 and will be remove in v1.5.0. Please, use ie_segment instead.
[WARNING] entropy_temp variable is deprecated and will be remove in next versions!. Please, use temperature variable instead
[WARNING] offset and probe are molsurf-only options
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/user/software/Amber20/amber20/bin/cpptraj
[INFO ] tleap found! Using /home/user/software/Amber20/amber20/bin/tleap
[INFO ] parmchk2 found! Using /home/user/software/Amber20/amber20/bin/parmchk2
[INFO ] mmpbsa_py_energy found! Using /home/user/software/Amber20/amber20/bin/mmpbsa_py_energy
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /usr/local/gromacs/bin/gmx
[INFO ] Checking external programs...Done.[INFO ] Building AMBER Topologies from GROMACS files...
[INFO ] Checking gmxMMPBSA data folder exists in Amber data...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Running command: echo name 1 GMXMMPBSA_REC\n name 14 GMXMMPBSA_LIG\n 1 | 14\n q\n | /usr/local/gromacs/bin/gmx make_ndx -n index.ndx -o _GMXMMPBSA_COM_index.ndx
[INFO ] Normal Complex: Saving group 1_14 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Running command: echo GMXMMPBSA_REC_GMXMMPBSA_LIG | /usr/local/gromacs/bin/gmx editconf -f md.tpr -o _GMXMMPBSA_COM.pdb -n _GMXMMPBSA_COM_index.ndx
[INFO ] Generating ligand parameters from UNK_bcc_gaff.mol2 file...
[INFO ] Running command: /home/user/software/Amber20/amber20/bin/parmchk2 -i UNK_bcc_gaff.mol2 -f mol2 -o _GMXMMPBSA_UNK_bcc_gaff.frcmod
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Complex: Saving group 1 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] Running command: echo 1 | /usr/local/gromacs/bin/gmx editconf -f md.tpr -o _GMXMMPBSA_REC.pdb -n _GMXMMPBSA_COM_index.ndx
[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 14 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO ] Running command: echo 14 | /usr/local/gromacs/bin/gmx editconf -f md.tpr -o _GMXMMPBSA_LIG.pdb -n _GMXMMPBSA_COM_index.ndx
[INFO ] Chains ID found. Ignoring chains ID assignation...
[INFO ] Generating AMBER Compatible PDB Files...
[INFO ] Building tleap input files...
[INFO ] Running command: /home/user/software/Amber20/amber20/bin/tleap -f _GMXMMPBSA_leap.in -I /home/user/anaconda3/lib/python3.7/site-packages/GMXMMPBSA/data
[INFO ] Cleaning normal complex trajectories...
[INFO ] Running command: echo GMXMMPBSA_REC_GMXMMPBSA_LIG | /usr/local/gromacs/bin/gmx trjconv -f fbd.xtc -s md.tpr -o COM_traj_0.xtc -n _GMXMMPBSA_COM_index.ndx
[INFO ] Building AMBER Topologies from GROMACS files...Done.[INFO ] Loading and checking parameter files for compatibility...Preparing trajectories for simulation...
/home/user/software/Amber20/amber20/bin/cpptraj: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directoryFile "/home/user/anaconda3/bin/gmx_MMPBSA", line 8, in <module>sys.exit(gmxmmpbsa())File "/home/user/anaconda3/lib/python3.7/site-packages/GMXMMPBSA/app.py", line 97, in gmxmmpbsaapp.file_setup()File "/home/user/anaconda3/lib/python3.7/site-packages/GMXMMPBSA/main.py", line 146, in file_setupself.external_progs['cpptraj'], self.pre)File "/home/user/anaconda3/lib/python3.7/site-packages/GMXMMPBSA/make_trajs.py", line 68, in make_trajectoriestraj = Trajectory(FILES.complex_prmtop, FILES.complex_trajs, cpptraj)File "/home/user/anaconda3/lib/python3.7/site-packages/GMXMMPBSA/make_trajs.py", line 471, in __init__self.Query()File "/home/user/anaconda3/lib/python3.7/site-packages/GMXMMPBSA/make_trajs.py", line 606, in Queryraise TrajError('%s failed when querying %s' % (self.exe, traj))
TrajError: /home/user/software/Amber20/amber20/bin/cpptraj failed when querying COM_traj_0.xtc
Exiting. All files have been retained.
1） 在路径/home/user/software/Amber20/amber20/lib/ 和 /home/user/software/Amber20/amber20/lib64/ 下均没有libgfortran.so.3
2） 在conda下有libgfortran.so.4.0.0
[userrr@localhost gmx_MMPBSA]$ ll /home/user/anaconda3/lib/libgfortran.so*
lrwxrwxrwx. 1 user user 20 May 28 02:50 /home/user/anaconda3/lib/libgfortran.so -> libgfortran.so.4.0.0
lrwxrwxrwx. 1 user user 20 May 28 02:50 /home/user/anaconda3/lib/libgfortran.so.4 -> libgfortran.so.4.0.0
-rwxrwxr-x. 2 user user 5925928 Aug 18 2018 /home/user/anaconda3/lib/libgfortran.so.4.0.03） /usr/lib64/路径下有libgfortran.so.5.0.0
[userrr@localhost gmx_MMPBSA]$ ll /usr/lib64/libgfortran.so.*
lrwxrwxrwx. 1 root root 20 Oct 12 2020 /usr/lib64/libgfortran.so.5 -> libgfortran.so.5.0.0
-rwxr-xr-x. 1 root root 2622416 Oct 12 2020 /usr/lib64/libgfortran.so.5.0.0解决办法：
libgfortran.so.3 安装网站
[userrr@localhost ~]$ sudo dnf install compat-libgfortran-48
[sudo] password for userrr:
Repository AppStream is listed more than once in the configuration
Repository extras is listed more than once in the configuration
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Repository centosplus is listed more than once in the configuration
Last metadata expiration check: 2:23:10 ago on Fri 23 Jul 2021 01:56:49 AM EDT.
Dependencies resolved.
=============================================================================================================================================================================================================================Package Arch Version Repository Size
=============================================================================================================================================================================================================================
Installing:compat-libgfortran-48 x86_64 4.8.5-36.1.el8 AppStream 275 kTransaction Summary
=============================================================================================================================================================================================================================
Install 1 PackageTotal download size: 275 k
Installed size: 1.1 M
Is this ok [y/N]: y
Downloading Packages:
compat-libgfortran-48-4.8.5-36.1.el8.x86_64.rpm 200 kB/s | 275 kB 00:01
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Total 57 kB/s | 275 kB 00:04
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transactionPreparing : 1/1Installing : compat-libgfortran-48-4.8.5-36.1.el8.x86_64 1/1Running scriptlet: compat-libgfortran-48-4.8.5-36.1.el8.x86_64 1/1
/sbin/ldconfig: /usr/local/cuda-11.2/targets/x86_64-linux/lib/libcudnn_ops_train.so.8 is not a symbolic link/sbin/ldconfig: /usr/local/cuda-11.2/targets/x86_64-linux/lib/libcudnn_ops_infer.so.8 is not a symbolic link/sbin/ldconfig: /usr/local/cuda-11.2/targets/x86_64-linux/lib/libcudnn_cnn_train.so.8 is not a symbolic link/sbin/ldconfig: /usr/local/cuda-11.2/targets/x86_64-linux/lib/libcudnn.so.8 is not a symbolic link/sbin/ldconfig: /usr/local/cuda-11.2/targets/x86_64-linux/lib/libcudnn_cnn_infer.so.8 is not a symbolic link/sbin/ldconfig: /usr/local/cuda-11.2/targets/x86_64-linux/lib/libcudnn_adv_train.so.8 is not a symbolic link/sbin/ldconfig: /usr/local/cuda-11.2/targets/x86_64-linux/lib/libcudnn_adv_infer.so.8 is not a symbolic link/sbin/ldconfig: /usr/local/cuda-11.2/targets/x86_64-linux/lib/libcudnn_ops_train.so.8 is not a symbolic link/sbin/ldconfig: /usr/local/cuda-11.2/targets/x86_64-linux/lib/libcudnn_ops_infer.so.8 is not a symbolic link/sbin/ldconfig: /usr/local/cuda-11.2/targets/x86_64-linux/lib/libcudnn_cnn_train.so.8 is not a symbolic link/sbin/ldconfig: /usr/local/cuda-11.2/targets/x86_64-linux/lib/libcudnn.so.8 is not a symbolic link/sbin/ldconfig: /usr/local/cuda-11.2/targets/x86_64-linux/lib/libcudnn_cnn_infer.so.8 is not a symbolic link/sbin/ldconfig: /usr/local/cuda-11.2/targets/x86_64-linux/lib/libcudnn_adv_train.so.8 is not a symbolic link/sbin/ldconfig: /usr/local/cuda-11.2/targets/x86_64-linux/lib/libcudnn_adv_infer.so.8 is not a symbolic linkVerifying : compat-libgfortran-48-4.8.5-36.1.el8.x86_64 1/1Installed:compat-libgfortran-48-4.8.5-36.1.el8.x86_64Complete!再次搜索/usr/lib/路径下的libgfortran.so.*，已经有了libgfortran.so.3
[userr@localhost gmx_MMPBSA]$ ll /usr/lib64/libgfortran.so.*
lrwxrwxrwx 1 root root 20 May 13 2019 /usr/lib64/libgfortran.so.3 -> libgfortran.so.3.0.0
-rwxr-xr-x 1 root root 1194336 May 13 2019 /usr/lib64/libgfortran.so.3.0.0
lrwxrwxrwx. 1 root root 20 Oct 12 2020 /usr/lib64/libgfortran.so.5 -> libgfortran.so.5.0.0
-rwxr-xr-x. 1 root root 2622416 Oct 12 2020 /usr/lib64/libgfortran.so.5.0.0运行gmx_MMPBSA:，没有报错，已经正常计算
[userrr@localhost gmx_MMPBSA]$ gmx_MMPBSA -O -i mmpbsa.in -cs md.tpr -ci index.ndx -cg 1 14 -ct fbd.xtc -lm UNK_bcc_gaff.mol2
[INFO ] Starting
[INFO ] Command-linegmx_MMPBSA -O -i mmpbsa.in -cs md.tpr -ci index.ndx -cg 1 14 -ct fbd.xtc -lm UNK_bcc_gaff.mol2[WARNING] protein_forcefield and ligand_forcefield variables are deprecate since version 1.4.1 and will be remove in the next version. Please, use forcefield instead.
[WARNING] entropy variable is deprecate since version 1.4.2 and will be remove in v1.5.0. Please, use qh_entropy for Quasi-Harmonic approximation and i_entropy for Interaction entropy approximation instead.
[WARNING] entropy_seg variable is deprecate since version 1.4.2 and will be remove in v1.5.0. Please, use ie_segment instead.
[WARNING] entropy_temp variable is deprecated and will be remove in next versions!. Please, use temperature variable instead
[WARNING] offset and probe are molsurf-only options
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/user/software/Amber20/amber20/bin/cpptraj
[INFO ] tleap found! Using /home/user/software/Amber20/amber20/bin/tleap
[INFO ] parmchk2 found! Using /home/user/software/Amber20/amber20/bin/parmchk2
[INFO ] mmpbsa_py_energy found! Using /home/user/software/Amber20/amber20/bin/mmpbsa_py_energy
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /usr/local/gromacs/bin/gmx
[INFO ] Checking external programs...Done.[INFO ] Building AMBER Topologies from GROMACS files...
[INFO ] Checking gmxMMPBSA data folder exists in Amber data...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Making gmx_MMPBSA index for complex...
[INFO ] Running command: echo name 1 GMXMMPBSA_REC\n name 14 GMXMMPBSA_LIG\n 1 | 14\n q\n | /usr/local/gromacs/bin/gmx make_ndx -n index.ndx -o _GMXMMPBSA_COM_index.ndx
[INFO ] Normal Complex: Saving group 1_14 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO ] Running command: echo GMXMMPBSA_REC_GMXMMPBSA_LIG | /usr/local/gromacs/bin/gmx editconf -f md.tpr -o _GMXMMPBSA_COM.pdb -n _GMXMMPBSA_COM_index.ndx
[INFO ] Generating ligand parameters from UNK_bcc_gaff.mol2 file...
[INFO ] Running command: /home/user/software/Amber20/amber20/bin/parmchk2 -i UNK_bcc_gaff.mol2 -f mol2 -o _GMXMMPBSA_UNK_bcc_gaff.frcmod
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Complex: Saving group 1 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO ] Running command: echo 1 | /usr/local/gromacs/bin/gmx editconf -f md.tpr -o _GMXMMPBSA_REC.pdb -n _GMXMMPBSA_COM_index.ndx
[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 14 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO ] Running command: echo 14 | /usr/local/gromacs/bin/gmx editconf -f md.tpr -o _GMXMMPBSA_LIG.pdb -n _GMXMMPBSA_COM_index.ndx
[INFO ] Chains ID found. Ignoring chains ID assignation...
[INFO ] Generating AMBER Compatible PDB Files...
[INFO ] Building tleap input files...
[INFO ] Running command: /home/user/software/Amber20/amber20/bin/tleap -f _GMXMMPBSA_leap.in -I /home/user/anaconda3/lib/python3.7/site-packages/GMXMMPBSA/data
[INFO ] Cleaning normal complex trajectories...
[INFO ] Running command: echo GMXMMPBSA_REC_GMXMMPBSA_LIG | /usr/local/gromacs/bin/gmx trjconv -f fbd.xtc -s md.tpr -o COM_traj_0.xtc -n _GMXMMPBSA_COM_index.ndx
[INFO ] Building AMBER Topologies from GROMACS files...Done.[INFO ] Loading and checking parameter files for compatibility...Preparing trajectories for simulation...
46 frames were processed by cpptraj for use in calculation.Running calculations on normal system...Beginning GB calculations with /home/user/software/Amber20/amber20/bin/mmpbsa_py_energycalculating complex contribution...calculating receptor contribution...calculating ligand contribution...Beginning PB calculations with /home/user/software/Amber20/amber20/bin/mmpbsa_py_energycalculating complex contribution...gmx-MMPBSA — error while loading shared libraries: libgfortran.so.3: cannot open shared object file相关推荐
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