CBMC_Info not specified

Dear Cassandra-Developers,

first of all I want to say sorry for giving you feedback so late. Unfortunately I had some bureaucratic difficulties the last couple
of weeks. The new script sent by Ryan for creating mcf-files for rigid molecules works fine.
At the moment I have some trouble to start the simulation for the rigid Dimerization Product of 1,3-Cyclodihexene. The creation of the mcf-file worked without any problems. But when I start the simulation, I get the following error:

CBMC_Info not specified
This error occurred in subroutine Get_CBMC_Info.
Fatal Error. Stopping program.

My pdb-file looks like this:

COMPND UNNAMED
AUTHOR GENERATED BY OPEN BABEL 2.3.2
HETATM 1 C LIG 1 -2.454 -0.621 0.450 1.00 0.00 C
HETATM 2 Si LIG 1 -2.429 0.860 0.178 1.00 0.00 Si
HETATM 3 Si LIG 1 -1.412 1.454 -0.452 1.00 0.00 Si
HETATM 4 Ge LIG 1 -0.144 0.762 -0.892 1.00 0.00 Ge
HETATM 5 Ge LIG 1 -0.186 -0.802 -0.790 1.00 0.00 Ge
HETATM 6 C LIG 1 -1.604 -1.371 -0.585 1.00 0.00 C
HETATM 7 Si LIG 1 0.717 -0.471 1.552 1.00 0.00 Si
HETATM 8 Ge LIG 1 0.863 -1.265 0.274 1.00 0.00 Ge
HETATM 9 C LIG 1 2.268 -0.935 -0.308 1.00 0.00 C
HETATM 10 Si LIG 1 0.844 0.852 1.393 1.00 0.00 Si
HETATM 11 Ge LIG 1 1.068 1.281 -0.039 1.00 0.00 Ge
HETATM 12 C LIG 1 2.360 0.595 -0.564 1.00 0.00 C
CONECT 1 6 2
CONECT 2 1 3
CONECT 3 2 4
CONECT 4 3 5 11
CONECT 5 4 6 8
CONECT 6 1 5
CONECT 7 8 10
CONECT 8 5 7 9
CONECT 9 8 12
CONECT 10 7 11
CONECT 11 4 10 12
CONECT 12 9 11
MASTER 0 0 0 0 0 0 0 0 12 0 12 0
END

I used Ge and Si just to distinguish the different UA-Types.

My mcf file looks like this:

!*******************************************************************************
!Molecular connectivity file for endo2.pdb
!*******************************************************************************
!Atom Format
!index type element mass charge type parameters
!type="LJ", parms=epsilon sigma

# Atom_Info
12
1 C C 12.000 0 LJ 52.500 3.910 ring
2 Si Si 13.000 0 LJ 47.000 3.730 ring
3 Si Si 13.000 0 LJ 47.000 3.730 ring
4 Ge Ge 13.000 0 LJ 10.000 4.650 ring
5 Ge Ge 13.000 0 LJ 10.000 4.650 ring
6 C C 12.000 0 LJ 52.500 3.910 ring
7 Si Si 13.000 0 LJ 47.000 3.730 ring
8 Ge Ge 13.000 0 LJ 10.000 4.650 ring
9 C C 12.000 0 LJ 52.500 3.910 ring
10 Si Si 13.000 0 LJ 47.000 3.730 ring
11 Ge Ge 13.000 0 LJ 10.000 4.650 ring
12 C C 12.000 0 LJ 52.500 3.910 ring

!Bond Format
!index i j type parameters
!type="fixed", parms=bondLength

# Bond_Info
14
1 1 6 fixed 1.540
2 1 2 fixed 1.510
3 2 3 fixed 1.340
4 3 4 fixed 1.510
5 4 5 fixed 1.570
6 4 11 fixed 1.570
7 5 6 fixed 1.550
8 5 8 fixed 1.570
9 7 8 fixed 1.510
10 7 10 fixed 1.340
11 8 9 fixed 1.550
12 9 12 fixed 1.540
13 10 11 fixed 1.510
14 11 12 fixed 1.550

!Angle Format
!index i j k type parameters
!type="fixed", parms=equilibrium_angle
!type="harmonic", parms=force_constant equilibrium_angle

# Angle_Info
20
1 6 1 2 fixed 110.46
2 1 2 3 fixed 122.36
3 2 3 4 fixed 124.96
4 3 4 5 fixed 114.56
5 3 4 11 fixed 114.56
6 5 4 11 fixed 108.50
7 4 5 6 fixed 108.19
8 4 5 8 fixed 108.50
9 6 5 8 fixed 108.19
10 1 6 5 fixed 108.90
11 8 7 10 fixed 124.96
12 5 8 7 fixed 114.56
13 5 8 9 fixed 108.19
14 7 8 9 fixed 107.00
15 8 9 12 fixed 108.90
16 7 10 11 fixed 124.96
17 4 11 10 fixed 114.56
18 4 11 12 fixed 108.19
19 10 11 12 fixed 107.00
20 9 12 11 fixed 108.90

# Dihedral_Info
0

# Improper_Info
0

!Fragment Format
!index number_of_atoms_in_fragment branch_point other_atoms

# Fragment_Info
2
1 8 1 6 5 4 3 2 8 11
2 8 11 10 7 8 9 12 4 5


# Fragment_Connectivity
1
1 1 2


END


My input file:

!*******************************************************************************
!
! This is an input file for united-atom for Dimerization product of Cyclodihexene .
!
!
!*******************************************************************************
# Run_Name
endo2_298.15

# Sim_Type
NPT_MC

# Nbr_Species
1

# VDW_Style
LJ cut_tail 20.0

# Charge_Style
NONE

# Intra_Scaling
0.0 0.0 0.0 0.0


# Mixing_Rule
LB

# Seed_Info
80411904 80411904

# Rcutoff_Low
1.0

# Pair_Energy
TRUE

# Molecule_Files
endo2.mcf 256

# Box_Info
1
CUBIC
50.00

# Temperature_Info
298.15

# Pressure_Info
1.0

# Move_Probability_Info

# Prob_Translation
0.45
1.0

# Prob_Rotation
0.45
180.0

# Prob_Volume
0.10
200.0

# Done_Probability_Info

# Bond_Prob_Cutoff
1.0E-10

# CBMC_Info
kappa_ins 12
kappa_rot 0
kappa_dih 12
rcut_cbmc 6.5

# Start_Type
make_config
256

# Run_Type
Equilibration 100 10

# Average_Info ( 0 == yes, 1 = No)
1

# Frequency_Info
freq_type none
Nthermofreq 100
Ncoordfreq 100
MCsteps 10000
# Done_Frequency_Info

# Property_Info 1 0
Energy_Total
Nmols
Density
Volume
Pressure

# Fragment_Files
endo2_1.dat 1
endo2_2.dat 2





END

For the rigid molecule I created the fragment files on my own.

The endo2_1.dat file looks like this:

1
298.15 0.0
C -2.454 -0.621 0.450
C -1.604 -1.371 -0.585
Ge -0.186 -0.802 -0.790
Ge -0.144 0.762 -0.892
Si -1.412 1.454 -0.452
Si -2.429 0.860 0.178
Ge 0.863 -1.265 0.274
Ge 1.068 1.281 -0.039

endo2_2.dat looks ĺike this:

1
298.15 0.0
Ge 1.068 1.281 -0.039
Si 0.844 0.852 1.393
Si 0.717 -0.471 1.552
Ge 0.863 -1.265 0.274
C 2.268 -0.935 -0.308
C 2.360 0.595 -0.564
Ge -0.144 0.762 -0.892
Ge -0.186 -0.802 -0.790


Does anyone know what I've done wrong. Thank you very much in advance.

Hi Ryan,

thanks a lot for your quick reply and your hints. It works fine now!

Best regards,
Mark