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

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我是靠谱客的博主清脆香菇，这篇文章主要介绍gmx-MMPBSA — error while loading shared libraries: libgfortran.so.3: cannot open shared object file，现在分享给大家，希望可以做个参考。

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：

复制代码

[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-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_RECn name 14 GMXMMPBSA_LIGn
1 | 14n qn | /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.

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[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-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_RECn name 14 GMXMMPBSA_LIGn
1 | 14n qn | /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

复制代码

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[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.4.0.0

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

复制代码

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[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

复制代码

[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
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!

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[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
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

复制代码

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[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

复制代码

[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-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_RECn name 14 GMXMMPBSA_LIGn
1 | 14n qn | /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...

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[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-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_RECn name 14 GMXMMPBSA_LIGn
1 | 14n qn | /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...