Dear All,
I am beginner to RASPA software. I am working on diffusion and storage of drugs within mofs.
At the starting kevel, I resieve an error and I dont solve it at all.
This is the error:
Error in CBMC growing scheme. No atoms can be grown, check the connectivity of your molecule
I checked all input files and those of them seems correct. How can I solve it?
Thanks for your time.
Best regards,
The most common reason is that your molecule contains a ring. RASPA can not handle flexible rings.
yes. I have a ring in my structure. but in molecule file, I define all of bonds as rigid. here is related molecule.def file.
# critical constants: Temperature [T], Pressure [Pa], and Acentric factor [-]
0.0
0.0
0.0
# Number Of Atoms
12
# Number of groups
1
# benzene-group
rigid
# number of atoms
12
# atomic positions
0 C_1 1.12695400 -0.52662000 0.00003600
1 C_2 0.74022900 0.86804700 -0.00025100
2 N_9 -0.63270700 1.05031900 0.00004500
3 C_3 -1.60631600 0.07351800 0.00032400
4 N_8 -1.12034000 -1.20461800 -0.00001400
5 C_4 0.21606200 -1.50781300 0.00001800
6 F 2.44045100 -0.78310800 0.00001600
7 O_10 1.51472900 1.81170200 0.00003900
8 H_N9 -0.96541400 2.01129200 -0.00000100
9 O_11 -2.79825200 0.33618100 -0.00012900
10 H_N8 -1.80442000 -1.95287400 -0.00024000
11 H_xyl 0.48371800 -2.55620700 -0.00016000
# Chiral centers Bond Bend UrayBradley InvBend Torsion Imp. Torsion Bond/Bond Stretch/Bend Bend/Bend Bend/Torsion IntraVDW IntraCoulomb
0 12 0 0 0 0 0 0 0 0 0 0 0
Bond stretch: atom n1-n2, type, parameters
0 1 RIGID_BOND
1 2 RIGID_BOND
2 3 RIGID_BOND
3 4 RIGID_BOND
4 5 RIGID_BOND
5 0 RIGID_BOND
6 0 RIGID_BOND
7 1 RIGID_BOND
8 2 RIGID_BOND
9 3 RIGID_BOND
10 4 RIGID_BOND
11 0 RIGID_BOND
# Number of config moves
0
Remove the empty line after "11 H_xyl 0.48371800 -2.55620700 -0.00016000"
thanks for your reply.
I corrected this, but at this time, after 1 hour, running finished without any output or other folders :-[ :-[
here is my trial running simulation.input file:
SimulationType MonteCarlo
NumberOfCycles 5000
NumberOfInitializationCycles 1000
RestartFile no
PrintEvery 100
ChargeMethod Ewald
ChargeFromChargeEquilibration yes
Forcefield local
CuttOffVDW 13
EwaldPrecision 1e-6
Framework 0
FrameworkName ZIF-8
UnitCells 2 2 2
ExternalTemperature 298.0
ExternalPressure 10000.0
ComputeNumberOfMoleculesHistogram yes
WriteNumberOfMoleculesHistogramEvery 100
Component 0 MoleculeName 5-flouracil
MoleculeDefinition CastilloVlugtCalero2009
IdealGasRosenbluthWeight 1.0
TranslationProbability 1.0
RotationProbability 1.0
RegrowProbability 1.0
ExtraFrameworkMolecule no
CreateNumberOfMolecules 0
in all of my runnings, I did not see any output file!
also, I did not see any error!
For our version of the code, this should not happen (on a standard unix system) and indicates something very strange on your system. Use a debugger to found out why it fails.
If you're using a version by other people (for example the numat github version) then it could be that their python additions might cause this problem.
I tried to install your version with python setup.py install command. but when I run the program, I recieve this error:
OSError: /usr/local/lib/python2.7/dist-packages/RASPA2-2.0.3-py2.7-linux-x86_64.egg/RASPA2/simulations/lib/libraspa2.py: invalid ELF header
We do not have anything to do with python (that is an addition by 'numat' and their github version).
For our version (see the manual) you install with:
1 ) rm -rf autom4te.cache
2 ) mkdir m4
3 ) aclocal
4 ) autoreconf -i
5 ) automake --add-missing
6 ) autoconf
7 ) ./configure --prefix=${RASPA_DIR}
or
./scripts/CompileScript/make-gcc-local
8 ) make
9 ) make install