Molconn-Z 3.50 Manual: Appendix VII

Appendix VII

Error Messages

Molconn-Z checks for some errors in the processing of the information from the Input .B File and the Options selected by the user. 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.

Whenever an error is encountered, the program writes an error message to the output .L file and then to continue with the computations so that the user may have additional information in the Output Listing File .L for locating the problem and making the appropriate changes.

Molconn-Z has provision for the user not electing to produce an .L file, in which case Molconn-Z creates a .MSG file for error messages. If there are not error messages, the .MSG file will be empty. The user should check the directory for this file when the .L file is not selected.

There are errors which do not create an message in the .L file. These are associated with errors in the file names for the .B, .L, .S and .E files. In these cases an error message is sent to the terminal screen and the user is given the option to correct the file name in an interactive manner. Those error messages are not treated in this appendix.

In each of the error messages below, the point of origin in the program is indicated by listing the subroutine which created the error message. This information may be helpful to the user in some cases. In others, if the user is unable to determine the cause of the error message, the user should contact Lowell H. Hall (Hall Associates Consulting) with the error message information.

In some cases the same error message may originate from more than one subroutine and in these cases all the subroutine references are given.

Error Message 1:                from MOLCONNZ

Error in the connection table.
Further processing of the molecule disconnected.

Comment : The indicated skeletal connections are not internally consistent as given in the molecule input file. Carefully check your input for this molecule.

Error Message 2:                from SETUP

End of File encountered in Input File
Data read terminated .. Calculations Proceeding
   Check Input File

Comment : The file terminator '-1' is missing. Examine the Input .B File and add the '-1' to the end of the file.

Error Message 3:               3 from SETUP
                              17 from SMILEFIL

End of File encountered in B File after NN atoms.
Attempting to process the molecule
   Check Input File

Comment : The molecule terminator '-1' is missing or some other problem which causes an 'end of file message', encountered after atom number NN.. Examine the Input .B File and put the '-1' at the end of the molecule in question. This error message is also printed in the Output Listing .L file so that the user may identify the molecule in process when the error occurred.

Error Message 4:              4 from SETUP
                             12 from MICRO
                             14 from CHXFIL
                             16 DRAWFIL
                             20 from SMILEFIL
                             28 from MOLFIL

The number of atoms in this molecule
                    EXCEEDS the limit : N
Skipping to next molecule

Comment : The number of atoms is too large. The present limit on number of atoms, N (default N = 100), is determined by the memory requirement and is set in the file PARAM.DAT. See Chapter 3.

Error Message 5:              from SETUP

Atom ( ZZ )  zz  is not in the List 
 Arbitrary Values Given for ZV AND Z
             Z =         ZV =

Comment : The offending atom number (ZZ) and symbol (zz) do not correspond to the atoms in the tested list for Chi indices. The program has supplied values as if the atoms have the atomic number and number of valence electrons given in the error message. The user must use only atoms in the list or, if another atom is necessary, the user must supply a valence delta value. (See Chapter 6.)

Error Message 6:              from SETUP

Atoms  ZZ  and  YY are not properly connected
Check the input for these atoms!

Comment : The offending atom numbers (YY and ZZ) are given. The corresponding atoms are not properly connected in the connection table in the input .B file. Probably the .B file shows one of the atoms connected to the other but not the reverse. Inspect the .B file and make corrections. Also examine the .L file for more complete information.

Error Message 7:            from SMILEFIL

The ring closure number % i 1s too large
The maximum allowed number is 50.
Please check the SMILES string and reenter.

Comment : Ring closure numbers may not exceed 50. Check your input SMILES string and correct the ring closure numbers. Then rerun MOLCONN-Z.

Error Message 8:            from SETUP

No user supplied value given
                  valence delta of Atom # ZZ
So, DV set to XXX

Comment : The program is expecting a user supplied valence delta value for atom number ZZ. Since the value was not given in the B File, the value XXX is supplied. Check the symbol of this atom for correctness. Check .B file to make sure that the molecule is set up properly and for typographical errors. This message is specific for the symbols H and Q.

Error Message 9:            from SETUP

Atom i is not in the parametrized list.  
The value 0.5 has been assigned to DV.

Comment : Check the input .B file for atom symbols. If the symbol is not in the parametrized list, then a user supplied valence delta value may be given, if using the MOLCONN input format.

Error Message 10:           from SETUP

** This error message no longer exists in the software. **

Error Message 11:          11 from MICRO
                           13 from CHXFIL
                           15 from DRAWFIL
                           27 from MOLFIL

The file name : xxxxxxxxxxxxxxxxxxxx 
in the .B file cannot be found.
Check the file name or directory and
correct the .B file before rerunning Molconn-Z.

Comment : In the list of file names (for molecule input files) the name given for the current molecule does not correspond to a name in the indicated directory. Check validity of the file name and make correction.

Error Message 12:

See # 4

Error Message 13:

See # 11

Error Message 14:

See # 4

Error Message 15:

See # 11

Error Message 16:

See # 4

Error Message 17:

See # 3

Error Message 18:          from SMILEFIL

The character(s) at position n in
the SMILES string were not valid
as atomic symbols: Z, ZZ

Comment: : Examine the SMILES code for the current molecule. The character at position n is not valid as an atomic symbol. Make appropriate correction.

Error Message 19:          from SMILEFIL

No valid symbol was found at string position n.

Comment: : Examine the SMILES code for the current molecule. The character at position n is not valid at all. Make appropriate correction.

Error Message 20:

See # 4

Error Message 21:          from SMILEFIL

Number of left parentheses, n1,
not equal to number of right parentheses, n2.
Please check SMILES string and re-enter.

Comment : Examine the SMILES string for the current molecule and count the number of parentheses. Make the appropriate correction.

Error Message 22:          from ANALYZE

** Incorrect Length of Symbol**
for Atom Number  ZZ

Comment : In the. B file an atom symbol for atom ZZ is longer than three characters. The symbol has temporarily been set to *** for easy identification in the output listing file .L. Check the .B file for legal symbols and for typographical errors.

Error Message 23:          from KAPPA

The values for atom z, # i, for
>ZV = XXX, H = yyy, D = zzz
are not encoded for Kappa values.

Comment : Check the list of atoms for which alpha values can be calculated. See Appendix V.

Error Message 24:          from SMILEFIL

No Kappa ALPHA value can be calculated for atom # i.
Please examine input carefully.

Comment : There is no alpha parameter for the computation of Kappa alpha indices for this atom. See Appendix V. Check your .B file for proper atom symbols.

Error Message 25:          from KAPPA

No Table KAPPA Alpha Value for Atom No. : YY
             Z = ZZ

Comment : For atom number YY with atomic number ZZ there is no alpha parameter for the computation of Kappa alpha indices. eck your .B file for proper atom symbols.

Error Message 26:          from DRAWFIL

The atomic symbol, zz, not recognized.
    Please check the input.

Comment : The atomic symbol is not in the accepted list for ChemDraw or may be a typographical error. Please check the input code and adjust the atomic symbol.

Error Message 27:

See # 11

Error Message 28:
See # 4

Error Message 29: from RINGS Number of ring subgraphs exceeds the array dimensions, MAXRING
Comment : The number of Ring/Chain subgraphs is greater than the permitted array size. The array size parameter MAXRING can be increased in PARAM.DAT and the program reinstalled. (See Chapter 3 for detailed information.) Or the molecule may have been coded improperly in the .B file to give the appearance of a large and/or complex molecule.

Error Message 30: from SMILEFIL Period found at position i after N atoms indicates a disconnected structure. Molconn-Z may not handle such structures well. Please reconsider this structure. However, Molconn-Z will attempt to interpret.
Comment : Disconnected structures are indicated with a period in SMILES for the presence of ions. Molconn-Z will attempt to process the larger fragment. If that is not satisfactory, you may have to consider another approach.

Error Message 31: from SMILEFIL The number of ring closure numbers is not even. Check the SMILES string and try again.
Comment : The encoding of rings in SMILES requires an even number of ring numbers. Check the SMILES string and try again.

Error Message 32: from SMILEFIL Ring Closure Number i is not even. It occurs N times. Repair SMILES string and try again.
Comment : Each ring closure number must occur an even number of times to encode ring closure properly. check the SMILES string and reenter the data.