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gmx-MMPBSA — error while loading shared libraries: libgfortran.so.3: cannot open shared object file

程序员文章站 2022-07-14 15:41:28
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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：

[[email protected] 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-line
  gmx_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 directory
  File "/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 gmxmmpbsa
    app.file_setup()
  File "/home/user/anaconda3/lib/python3.7/site-packages/GMXMMPBSA/main.py", line 146, in file_setup
    self.external_progs['cpptraj'], self.pre)
  File "/home/user/anaconda3/lib/python3.7/site-packages/GMXMMPBSA/make_trajs.py", line 68, in make_trajectories
    traj = 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 Query
    raise 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

[[email protected] 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.4.0.0

3） /usr/lib64/路径下有libgfortran.so.5.0.0

[[email protected] 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

[[email protected] ~]$ 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
Repository PowerTools is listed more than once in the configuration
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 k

Transaction Summary
=============================================================================================================================================================================================================================
Install  1 Package

Total 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 transaction
  Preparing        :                                                                                                                                                                                                     1/1
  Installing       : compat-libgfortran-48-4.8.5-36.1.el8.x86_64                                                                                                                                                         1/1
  Running 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 link


  Verifying        : compat-libgfortran-48-4.8.5-36.1.el8.x86_64                                                                                                                                                         1/1

Installed:
  compat-libgfortran-48-4.8.5-36.1.el8.x86_64

Complete!

再次搜索/usr/lib/路径下的libgfortran.so.*，已经有了libgfortran.so.3

[[email protected] 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

[[email protected] 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-line
  gmx_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_energy
  calculating complex contribution...
  calculating receptor contribution...
  calculating ligand contribution...

Beginning PB calculations with /home/user/software/Amber20/amber20/bin/mmpbsa_py_energy
  calculating complex contribution...
相关标签： gmx_MMPBSA 日记 gfortran centos gromacs linux

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