Hi again,

I have tried to solve the problem that I described last Friday but without success. I was looking more carefully the log file (that was submitted in my first post) and there is something really strange. Maybe some of the more expert users could help me with this. When the program starts to run it generate a file pkci (that is the name of my sequence) that contains coordinates for the model. I assume this is the ini file (I am not sure why the ini extension is omitted). The number of atoms in this file is 890 (including 2 Zn atoms). I used this file to extract the ID for the residues coordinated with the Zn, information that is input in the ali file. The special restraints are read correctly as is evident from the log file:

Dynamically allocated memory at         amaxseq [B,kB,MB]:      5097041    4977.579     4.861

TOP_________>   216  163 CALL ROUTINE = 'special_restraints'

TOP_________>   217  756 ADD_RESTRAINT ATOM_IDS = 'SG:14' 'ZN:55', RESTRAINT_PARAM;

                      ETERS = 2 1 1 22 2 2 0 3.5 0.1

Dynamically allocated memory at        amprmcns [B,kB,MB]:      5097191    4977.726     4.861

TOP_________>   218  757 ADD_RESTRAINT ATOM_IDS = 'SG:17' 'ZN:55', RESTRAINT_PARAM;

                      ETERS = 2 1 1 22 2 2 0 3.5 0.1

Dynamically allocated memory at        amprmcns [B,kB,MB]:      5097191    4977.726     4.861

TOP_________>   219  758 ADD_RESTRAINT ATOM_IDS = 'NE2:39' 'ZN:55', RESTRAINT_PARA;

                      METERS = 2 1 1 22 2 2 0 3.5 0.1

Dynamically allocated memory at        amprmcns [B,kB,MB]:      5097191    4977.726     4.861

TOP_________>   220  759 ADD_RESTRAINT ATOM_IDS = 'SG:42' 'ZN:55', RESTRAINT_PARAM;

                      ETERS = 2 1 1 22 2 2 0 3.5 0.1

Dynamically allocated memory at        amprmcns [B,kB,MB]:      5097191    4977.726     4.861

TOP_________>   221  760 ADD_RESTRAINT ATOM_IDS = 'SG:31' 'ZN:54', RESTRAINT_PARAM;

                      ETERS = 2 1 1 22 2 2 0 3.5 0.1

Dynamically allocated memory at        amprmcns [B,kB,MB]:      5097191    4977.726     4.861

TOP_________>   222  761 ADD_RESTRAINT ATOM_IDS = 'SG:34' 'ZN:54', RESTRAINT_PARAM;

                      ETERS = 2 1 1 22 2 2 0 3.5 0.1

Dynamically allocated memory at        amprmcns [B,kB,MB]:      5097191    4977.726     4.861

TOP_________>   223  762 ADD_RESTRAINT ATOM_IDS = 'SG:50' 'ZN:54', RESTRAINT_PARAM;

                      ETERS = 2 1 1 22 2 2 0 3.5 0.1

Dynamically allocated memory at        amprmcns [B,kB,MB]:      5097191    4977.726     4.861

TOP_________>   224  763 ADD_RESTRAINT ATOM_IDS = 'NE2:53' 'ZN:54', RESTRAINT_PARA;

                      METERS = 2 1 1 22 2 2 0 3.5 0.1

After that the model file is read again:

openf5__224_> Open       18  UNKNOWN  SEQUENTIAL  pkci.D00000001

TOP_________>   243  218 READ_MODEL FILE = MODEL

openf5__224_> Open       11  OLD  SEQUENTIAL  pkci.ini

openf5__224_> Open       11  OLD  SEQUENTIAL  pkci.ini

rdatm___297_> Segments, residues, atoms:        2       55      438

rdatm___298_> Segment:        1     1    53      436

rdatm___298_> Segment:        2    54    55        2

TOP_________>   244  219 CALL ROUTINE = 'select_atoms'

But the strange thing is that the number of atoms in the file is 438 not 890 as in the pkci file generated initially

So after a few lines the log file gives an out of bounds message:

csrrng__299E> Atom index is out of bounds:      441      438

Any ideas of what is going on here? By the way, I am running in windows.

Thanks

Alfredo Cardenas