error in generating species files.
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8 years 8 months ago #48
by gandhiforbes
Dear Sir,
I have generated pdb,ff,mcf and inp files. After that, i am using the following command:
python ./library_setup.py /home/Downloads/FlareGet/Cassandra_V1.0/Src/cassandra_gfortran.exe pentane.inp pentane.pdb
and i am getting the following messages:
*********Cassandra setup*********
Cassandra location: /home/Downloads/FlareGet/Cassandra_V1.0/Src/cassandra_gfortran.exe
Scanning input file...
Number of species found: 1
The MCF file number 1 is: pentane.mcf
Species 1 has 3 fragments
Molecules with rings found. These are:
Species 1 has 0 rings.
Creating input MCF generation file for species 1...
Done...
Running Cassandra to generate MCF files...
Traceback (most recent call last):
File "./library_setup.py", line 405, in <module>
subprocess.call([cassandra_location,'species'+str(i+1)+'_mcf_gen.inp'])
File "/usr/lib/python2.7/subprocess.py", line 522, in call
return Popen(*popenargs, **kwargs).wait()
File "/usr/lib/python2.7/subprocess.py", line 710, in __init__
errread, errwrite)
File "/usr/lib/python2.7/subprocess.py", line 1327, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
how to solve this problem?
Regards,
Anand Bharti
I have generated pdb,ff,mcf and inp files. After that, i am using the following command:
python ./library_setup.py /home/Downloads/FlareGet/Cassandra_V1.0/Src/cassandra_gfortran.exe pentane.inp pentane.pdb
and i am getting the following messages:
*********Cassandra setup*********
Cassandra location: /home/Downloads/FlareGet/Cassandra_V1.0/Src/cassandra_gfortran.exe
Scanning input file...
Number of species found: 1
The MCF file number 1 is: pentane.mcf
Species 1 has 3 fragments
Molecules with rings found. These are:
Species 1 has 0 rings.
Creating input MCF generation file for species 1...
Done...
Running Cassandra to generate MCF files...
Traceback (most recent call last):
File "./library_setup.py", line 405, in <module>
subprocess.call([cassandra_location,'species'+str(i+1)+'_mcf_gen.inp'])
File "/usr/lib/python2.7/subprocess.py", line 522, in call
return Popen(*popenargs, **kwargs).wait()
File "/usr/lib/python2.7/subprocess.py", line 710, in __init__
errread, errwrite)
File "/usr/lib/python2.7/subprocess.py", line 1327, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory
how to solve this problem?
Regards,
Anand Bharti
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8 years 8 months ago #50
by gandhiforbes
PDB FILE:
COMPND UNNAMED
AUTHOR GENERATED BY OPEN BABEL 2.3.2
HETATM 1 C LIG 1 -3.495 0.602 -0.000 1.00 0.00 C CH3
HETATM 2 C LIG 1 -2.125 -0.043 0.000 1.00 0.00 C CH2
HETATM 3 O LIG 1 -1.144 0.947 -0.000 1.00 0.00 O
HETATM 4 C LIG 1 0.062 0.248 -0.000 1.00 0.00 C CH2
HETATM 5 C LIG 1 1.215 1.229 -0.000 1.00 0.00 C CH3
CONECT 1 2
CONECT 2 1 3
CONECT 3 2 4
CONECT 4 3 5
CONECT 5 4
MASTER 0 0 0 0 0 0 0 0 5 0 5 0
END
MCF FILE:
!**********************************************************************************
!Molecular connectivity file for DEE.pdb
!**********************************************************************************
# Atom_Info
5
1 C1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1 C 15 0.000 LJ 98.0 3.750
2 C2_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1 C 14 0.250 LJ 46.0 3.950
3 O3_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1 O 16 -0.500 LJ 55.0 2.800
4 C4_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1 C 14 0.250 LJ 46.0 3.950
5 C5_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1 C 15 0.000 LJ 98.0 3.750
# Bond_Info
4
1 1 2 fixed 1.540
2 2 3 fixed 1.410
3 3 4 fixed 1.410
4 4 5 fixed 1.540
# Angle_Info
3
1 1 2 3 harmonic 112.0
2 2 3 4 harmonic 112.0
3 3 4 5 harmonic 112.0
# Dihedral_Info
2
1 1 2 3 4 OPLS 0.00000 6.03056 -1.35809 4.64087
2 2 3 4 5 OPLS 0.00000 6.03056 -1.35809 4.64087
# Fragment_Info
3
1 3 2 1 3
2 3 3 2 4
3 3 4 3 5
# Improper_Info
0
# Fragment_Connectivity
2
1 1 2
2 2 3
END
INP FILE:
! This is the input file for GEMC simulation of diethylether at 343.15 K
# Run_Name
DEE
!
# Sim_Type
GEMC
!
# Nbr_Species
1
!
# VDW_Style
LJ cut_tail 14.0
LJ cut_tail 14.0
!
# Rcutoff_Low
1.0
!
# Mixing_Rule
LB
!
# Charge_Style
coul Ewald 14.0 0.000001
coul Ewald 14.0 0.000001
!
# Intra_Scaling
0.0 0.0 0.0 1.0
0.0 0.0 0.0 1.0
!
# Molecule_Files
DEE.mcf 300
!
# Box_Info
2
CUBIC
35.2911 35.2911 35.2911
CUBIC
92.5596 92.5596 92.5596
!
# Temperature_Info
343.15 343.15
!
# Seed_Info
200 24000
!
# Move_Probability_Info
# Prob_Translation
0.30
0.4265
14.0
# Prob_Rotation
0.30
38.0
180.0
# Prob_Regrowth
0.30
1.0
# Prob_Volume
0.005
900.0
900.0
# Prob_Swap
0.095
insertion method
reservoir
# Done_Probability_Info
!
# Pressure_Info
1.0
# Bond_Prob_Cutoff
1.0E-10
# CBMC_Info
kappa_ins 12
kappa_rot 0
kappa_dih 12
rcut_cbmc 6.5 6.5
# Start_Type
make_config
200 100
!
# Run_Type
Production 5000 100
!
# Average_Info ( 0 == yes, 1 = No)
1
# Frequency_Info
freq_type none
Nthermofreq 300
Ncoordfreq 3000
MCsteps 3000
# Done_Frequency_Info
!
# Property_Info 1
Energy_Total
Nmols
Volume
# Property_Info 2
Energy_Total
Nmols
Volume
Pressure
# Fragment_Files
species1/frag1/frag1.dat 1
species1/frag2/frag2.dat 2
species1/frag3/frag3.dat 3
# Pair_Energy
TRUE
END
Thanks.
COMPND UNNAMED
AUTHOR GENERATED BY OPEN BABEL 2.3.2
HETATM 1 C LIG 1 -3.495 0.602 -0.000 1.00 0.00 C CH3
HETATM 2 C LIG 1 -2.125 -0.043 0.000 1.00 0.00 C CH2
HETATM 3 O LIG 1 -1.144 0.947 -0.000 1.00 0.00 O
HETATM 4 C LIG 1 0.062 0.248 -0.000 1.00 0.00 C CH2
HETATM 5 C LIG 1 1.215 1.229 -0.000 1.00 0.00 C CH3
CONECT 1 2
CONECT 2 1 3
CONECT 3 2 4
CONECT 4 3 5
CONECT 5 4
MASTER 0 0 0 0 0 0 0 0 5 0 5 0
END
MCF FILE:
!**********************************************************************************
!Molecular connectivity file for DEE.pdb
!**********************************************************************************
# Atom_Info
5
1 C1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1 C 15 0.000 LJ 98.0 3.750
2 C2_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1 C 14 0.250 LJ 46.0 3.950
3 O3_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1 O 16 -0.500 LJ 55.0 2.800
4 C4_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1 C 14 0.250 LJ 46.0 3.950
5 C5_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1_s1 C 15 0.000 LJ 98.0 3.750
# Bond_Info
4
1 1 2 fixed 1.540
2 2 3 fixed 1.410
3 3 4 fixed 1.410
4 4 5 fixed 1.540
# Angle_Info
3
1 1 2 3 harmonic 112.0
2 2 3 4 harmonic 112.0
3 3 4 5 harmonic 112.0
# Dihedral_Info
2
1 1 2 3 4 OPLS 0.00000 6.03056 -1.35809 4.64087
2 2 3 4 5 OPLS 0.00000 6.03056 -1.35809 4.64087
# Fragment_Info
3
1 3 2 1 3
2 3 3 2 4
3 3 4 3 5
# Improper_Info
0
# Fragment_Connectivity
2
1 1 2
2 2 3
END
INP FILE:
! This is the input file for GEMC simulation of diethylether at 343.15 K
# Run_Name
DEE
!
# Sim_Type
GEMC
!
# Nbr_Species
1
!
# VDW_Style
LJ cut_tail 14.0
LJ cut_tail 14.0
!
# Rcutoff_Low
1.0
!
# Mixing_Rule
LB
!
# Charge_Style
coul Ewald 14.0 0.000001
coul Ewald 14.0 0.000001
!
# Intra_Scaling
0.0 0.0 0.0 1.0
0.0 0.0 0.0 1.0
!
# Molecule_Files
DEE.mcf 300
!
# Box_Info
2
CUBIC
35.2911 35.2911 35.2911
CUBIC
92.5596 92.5596 92.5596
!
# Temperature_Info
343.15 343.15
!
# Seed_Info
200 24000
!
# Move_Probability_Info
# Prob_Translation
0.30
0.4265
14.0
# Prob_Rotation
0.30
38.0
180.0
# Prob_Regrowth
0.30
1.0
# Prob_Volume
0.005
900.0
900.0
# Prob_Swap
0.095
insertion method
reservoir
# Done_Probability_Info
!
# Pressure_Info
1.0
# Bond_Prob_Cutoff
1.0E-10
# CBMC_Info
kappa_ins 12
kappa_rot 0
kappa_dih 12
rcut_cbmc 6.5 6.5
# Start_Type
make_config
200 100
!
# Run_Type
Production 5000 100
!
# Average_Info ( 0 == yes, 1 = No)
1
# Frequency_Info
freq_type none
Nthermofreq 300
Ncoordfreq 3000
MCsteps 3000
# Done_Frequency_Info
!
# Property_Info 1
Energy_Total
Nmols
Volume
# Property_Info 2
Energy_Total
Nmols
Volume
Pressure
# Fragment_Files
species1/frag1/frag1.dat 1
species1/frag2/frag2.dat 2
species1/frag3/frag3.dat 3
# Pair_Energy
TRUE
END
Thanks.
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8 years 8 months ago #51
by ryangmullen
Your files look fine, but I note they reference files DEE.pdb and DEE.mcf, whereas in your original post you reference files pentane.inp, pentane.mcf and pentane.pdb. What system are you simulating, pentane or DEE?
With the DEE files, the library_setup.py script runs fine for me. I can only reproduce your error if I call the library_setup.py with a cassandra executable that doesn't exist. Can you verify that you have the following file?
/home/Downloads/FlareGet/Cassandra_V1.0/Src/cassandra_gfortran.exe
With the DEE files, the library_setup.py script runs fine for me. I can only reproduce your error if I call the library_setup.py with a cassandra executable that doesn't exist. Can you verify that you have the following file?
/home/Downloads/FlareGet/Cassandra_V1.0/Src/cassandra_gfortran.exe
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