Problem with creating fragment library

Dear Cassandra-Developer, dear users,


I would like to use cassandra for my Ph.D. thesis. I tried some of the examples which worked well.
Unfortunately when I try to create a fragment library for my own molecule (e.g. cyclopentane) I get the following error:

mark@mark-desktop:~/Cassandra_V1.0/Scripts/Frag_Library_Setup$ python library_setup.py /home/mark/Cassandra_V1.0/Src/cassandra_gfortran.exe cyclopentan.inp cyclopentan.pdb

*********Cassandra setup*********

Cassandra location: /home/mark/Cassandra_V1.0/Src/cassandra_gfortran.exe
Scanning input file...
Number of species found: 1
The MCF file number 1 is: cyclopentan.mcf
Species 1 has 1 fragments
Molecules with rings found. These are:
Species 1 has 1 rings.


Creating input MCF generation file for species 1...
Done...
Running Cassandra to generate MCF files...
At line 1308 of file participation.f90 (unit = 204, file = 'XTY�XTY�')
Fortran runtime error: File already opened in another unit
Done...
Generating RING FRAGMENT library species 1 fragment 1
Error! In mcf file
../fragments/frag_1_1.mcf
nbonds field not present
nangles field not present
ndihedrals field not present
nimpropers field not present
This error occurred in subroutine Get_Init_Params.
Fatal Error. Stopping program.
Removing temporary input file
Finished
mark@mark-desktop:~/Cassandra_V1.0/Scripts/Frag_Library_Setup$

The creation of the ff-file and the mcf-file worked without any problems. The input-file, ff-file, pdb-file and mcf-file are in the attachment.

Another question is the building of rigid molecules like Trappe-UA-Benzene molecules. When I create the the ff-file I typed "none" for the diheder-type. When I try to create the Fragment-file I get the following error:

*********Cassandra setup*********

Cassandra location: /home/mark/Cassandra_V1.0/Src/cassandra_gfortran.exe
Scanning input file...
Number of species found: 1
The MCF file number 1 is: benzene.mcf
Species 1 has 1 fragments
Molecules with rings found. These are:
Species 1 has 1 rings.


Creating input MCF generation file for species 1...
Done...
Running Cassandra to generate MCF files...
Expected at least 6 input(s) on line 33 of input file.
This error occurred in subroutine Parse_String.
Fatal Error. Stopping program.
Done...
Generating RING FRAGMENT library species 1 fragment 1
Unable to open molecular connectivity file.
This error occurred in subroutine Get_Molecule_Info.
Fatal Error. Stopping program.
Removing temporary input file
Finished
mark@mark-desktop:~/Cassandra_V1.0/Scripts/Frag_Library_Setup$

The ff-file, mcf-file and input-file are in the attachment.
My system is Ubuntu 14.04 LTS 32 bit.
I hope I didn't ask too many or/and awkward questions and somebody could give me some
advice.

Many thanks in advance,
Mark

OK, thank you very much for your efforts.

Greetings,
Mark

Hi Ryan,

thank you for your quick reply. I would be happy, if you could send me the new version of the script, so I wrote you an Email.
Here is my pdb-file created with Avogadro (United Atom):

COMPND UNNAMED
AUTHOR GENERATED BY OPEN BABEL 2.3.2
ATOM 1 C LIG 1 -0.484 1.004 0.646 1.00 0.00 C
ATOM 2 C LIG 1 0.557 1.066 -0.466 1.00 0.00 C
ATOM 3 C LIG 1 0.988 -0.372 -0.744 1.00 0.00 C
ATOM 4 C LIG 1 0.002 -1.291 -0.025 1.00 0.00 C
ATOM 5 C LIG 1 -1.071 -0.401 0.596 1.00 0.00 C
CONECT 1 2 5
CONECT 2 1 3
CONECT 3 2 4
CONECT 4 3 5
CONECT 5 1 4
MASTER 0 0 0 0 0 0 0 0 5 0 5 0
END

My ff-file with added values :

atomtypes
1

begin atom-atomtype
1 C
2 C
3 C
4 C
5 C
end atom-atomtype

dihedraltype OPLS

nonbonded
C
Sigma 3.88
Epsilon 56.33

bonds
C C
Length 1.54
Constant fixed

angles
C C C
Angle 105.5
Constant 31250.0

dihedrals
C C C C
a0 31394.0
a1 45914.0
a2 16518.0
a3 1496.0

charge
1 0

charge
2 0

charge
3 0

charge
4 0

charge
5 0

end

My mcf-file looks like this:

!**********************************************************************************
!Molecular connectivity file for cyclohexane.pdb
!**********************************************************************************

# Atom_Info
6
1 C1 C 14.0000 0 LJ 52.5 3.91 ring
2 C2 C 14.0000 0 LJ 52.5 3.91 ring
3 C3 C 14.0000 0 LJ 52.5 3.91 ring
4 C4 C 14.0000 0 LJ 52.5 3.91 ring
5 C5 C 14.0000 0 LJ 52.5 3.91 ring
6 C6 C 14.0000 0 LJ 52.5 3.91 ring

# Bond_Info
6
1 1 2 fixed 1.54
2 1 3 fixed 1.54
3 2 5 fixed 1.54
4 3 4 fixed 1.54
5 4 6 fixed 1.54
6 5 6 fixed 1.54

# Angle_Info
6
1 2 1 3 harmonic 31250.0 114.0
2 1 2 5 harmonic 31250.0 114.0
3 1 3 4 harmonic 31250.0 114.0
4 3 4 6 harmonic 31250.0 114.0
5 2 5 6 harmonic 31250.0 114.0
6 4 6 5 harmonic 31250.0 114.0

# Dihedral_Info
6
1 1 2 5 6 OPLS 42.17 56.86 29.17 0.5237
2 1 3 4 6 OPLS 42.17 56.86 29.17 0.5237
3 2 1 3 4 OPLS 42.17 56.86 29.17 0.5237
4 2 5 6 4 OPLS 42.17 56.86 29.17 0.5237
5 3 1 2 5 OPLS 42.17 56.86 29.17 0.5237
6 3 4 6 5 OPLS 42.17 56.86 29.17 0.5237

# Fragment_Info
1
1 6 1 2 5 6 4 3

# Improper_Info
0

# Fragment_Connectivity
0


END

I hope I didn't forget anything.

Best regards,
Mark