Molconn-Z checks for some errors in the processing of the information from the Input Molecular Structure File and the Options selected by the user in the Control File. No attempt has been made to check for all conceivable problems. Some common and more serious errors have been anticipated. Following is a list of error messages along with indications of possible causes of the error. Control of error information is provided by the keywords WARNINGS (on or off) and ERRORS (exit, skip, contine) in the control file. Errors and warnings are printed only to the standard out.
License Errors
No eduSoft License or incorrect
eduSoft License
Invalid
License key: Molconnz!
Some possibilities: a) Verify the
environmental variable $MCONN_LICENSE is set to the
proper file, e.g.,
/usr/eduSoft/molconnz4.03/MolconnZLicense.dat.
b) There is a mismatch between the hostname of this computer and
the hostname used to create your license key.
See the License
Instructions at
http://www.edusoft-lc.com/license/key_inst.html
c) The actual key is ONLY the short string BETWEEN the '' in the
license file we sent you -- all of the other
data in the file is
for information
purposes only. Only the key(s) should be copied
to the appropriate license file.
d)
Please contact eduSoft LC with other licensing questions:
http://www.edusoft-lc.com/contact.html
No Daylight License or incorrect
Daylight License
Invalid
license: can't open license file
("/usr/local/Daylightlicense.dat")
Contact Daylight
Support for assistance:
phone: 1-949-367-9990 FAX:
1-949-367-0990
email: info@daylight.com
The eduSoft license file is found from the environment variable MCONN_LICENSE. Check this file by listing the file with cat $MCONN_LICENSE to make sure it contains a single line with has as it first word your hostname. Similarly for the Daylight license, this file is located with the environmental variable DY_LICENSEDATA.
Control File Keyword Errors
Invalid input format type in control.dat:
Molconnz does not recognize input
format type.
Molconnz cannot proceed without a INPUTFORMAT
specification!
The file type defined by the INPUTFORMAT keyword must mach with the file type that is presented with the second argument to the molconnz command. Be very careful with this as it could also cause a core dump that results from the OELIB code.
Complex Molecule Errors
Some complex molecules could result in one of the following errors:
Error: Disconnected Graph! Molecule is skipped.
Molconn-Z can not deal with non-bonded structures.
The most common of these are salts. Typically, salts consist of 2 components,
the anion and the cation. Usually one is a simple un-interesting structure
and can be ignored. However, the user must edit the structure (SMILES or other)
to remove this un-interesting component of the salt. Then a charge would
probably need to be added. If both cation and anion have interesting structures,
then one might separate the salt into 2 separate structures for Molconn-Z.
Error: Disconnected Graph! Reconstitution into ion graphs will be attempted.
A new feature in Molconn-Z 4.10 is the "fix" option on ERRORS which will
attempt to do a Molconn-Z analysis on the separate components of the salt.
Frequently, a salt may contain an uninteresting counterion like sodium. If this
is the case a new error message is encountered:
Error: Molecule is (heavy atom) monoatomic: No bonds! Molecule is skipped.
Warning: Unexpectedly high valence for atom 14! Check structure.
Some molecules can only be properly represented by multiple
resonance structures. When only one resonance structure is represented,
the bonding may appear to be outside the norms. You should verify that
the structure has the resonance structure you wish to study, but the
Molconn-Z calculation will continue properly.
Error: Pathcount buffer reached! Molecule is skipped.
Some large structures with many rings can swamp the count of
paths between 2 atoms. This structure is probably too complex for
Molconn-Z. If you verify that it is a good structure and does
not appear overly complex, please let us know and perhaps we can help.
Error: Unexpected number of bonds to atom 6. Structure rejected!
The molecular structure has been interpreted to have an unexpected number
of bonds to an atom. This can happen if this is an organometalic with more than
8 "bonds", or it can happen because the structure file is in error or it
could happen because the structure interpretor (particularly OELIB) had dealt
with the structure incorrectly. In any event it results in a structure file
read error.
Atomic number 0 outside of range! Atom element now Du
Some programs (like Sybyl) can assign non-real atoms to
coordinate positions, but they will have odd atomic numbers (like 0).
Molconn-Z assigns these a "dummy" atom type.
Molconn-Z is not designed for very large molecules. These could result in errors:
No paths
found with length < Maximum Chi Order (99)!
If you are getting these errors and you know you have a reasonable-sized molecule and it's structure file is not in error or corrupt, please contact eduSoft, for help with your problem.
Whenever an error is encountered, the program writes an error message to the standard out (usually the terminal screen). In addition, for certain errors, it will put an "errorcode" value into the outfile. This value is the second field in the CSVUSEFUL output format. For the S Record format (Record 1 or ALLRECORDS) this value will be placed in the 7th field where there normally would be the value for "nclass". The table of those values is below.
| ESLC_MOLCONNZ_ERROR_CIRCUITBUFFEROVERFLOW | 1 |
| ESLC_MOLCONNZ_ERROR_PATHBUFFEROVERFLOW | 2 |
| ESLC_MOLCONNZ_ERROR_DISCONNECTEDGRAPH | 3 |
| ESLC_MOLCONNZ_ERROR_EDGESOVERFLOW | 4 |
| ESLC_MOLCONNZ_ERROR_MONOATOMIC_MOLECULE | 5 |
| ESLC_MOLCONNZ_ERROR_UNPARAMETERIZED_ELEMENT | 6 |
| ESLC_MOLCONNZ_ERROR_FILE_READ_FAILURE | 90 |