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