MPACK step by step

[Using MPACK is simple if proper inputs are created adhering to rules. The user simply interacts with questions. An interactive session with typical questions from MPACK is described below]
Start the mpack script by calling    : mpack

Type core name of the output file : This will be used for creating different output files. Use simple names like model1 or mod1. Do not use extensions or other fancy characters!

Do you have a toplogy file: (y/n) ?
Say yes if you would like to use a topology file to derive approximate constraints. You must adhere to the topology file format.

Do you have a template to extract constraints from ?
   If you have a template to extract constraints from enter ‘y’. Please note the first template used should correspond to your master alignment.

Name of the seq. align. file ?
  Enter your sequence alignment file name. The alignment file must have an extension *.aln and should be in clustalw format as explained in the alignment rules.

Enter the name of the pdb file ?
Enter the pdb file name, must have an extension *.pdb and should have exactly the residues contained in the alignment file. 

Enter interval (deg) for PSI/PHI (default 10):
 Upper/lower intervals for dihedral angles. You can change the default values.

Enter interval (deg) for OMEGA (default 5):
   Upper/lower intervals for OMEGA dihedral angle. Note currently if the residues don’t match in the alignment and if the template consists of CISPEP then manually one should edit the OMEGA angle (* appropriately and rerun * script.

Number of distance constraints per atom (default 30 15 12.5) :
  Specify the number of constraints you would like to extract per atom. You can specify higher number if the length of the protein (alignment) is small.  Higher number of the constraints will compromise the execution time of the program so do not exceed more that 30 unless you have 5-15 residue template fragment from which you want to extract constraints.

Enter threshold between upper and lower limits (default 0.5) :
 Specify the threshold of upper and lower limits, increase threshold if you like to have more flexibility (generally the case if the % id between the template and target is low) and  reduce it if the proteins are highly similar. Most cases the default value is fine.

Do you like to specify fragments ?
  If you like to manually specify fragments to be used in the modeling then enter yes. But it is advised to use the automatic option for specifying the fragments so type ‘n’.

Do you have another template to extract constraints from (y/n) ?
 If you have multiple template specify yes. The start residue number corresponding the master alignment should be noted down.

Enter the starting residue number of the target sequence in the alignment file ?
Enter the starting residue number. Next sequence of  questions will be similar to the above. If you answered no (by specifying ‘n’) for the question do you have another template to extract constraints from….. then

Do you have disulphide bonds in the target ?
 If you have disulphide bonds (you must have already changed in the alignment ‘C’ to ‘c’, otherwise you must edit the alignment file and restart the program.  You will also be required to know the residue pairs involved in the CYSS bonds.  If you answer ‘y’ then

No. of SS bonds ?
     Specify number of disulphide bonds

Enter res. In 1 SSBND ?  (RES1, RES2)  Enter residues involved in the 1st SSBOND with RES1 <RES2.

Do you want to run DIAMOD ?
 If you say "yes" it will prepare input files for DIAMOD.

How many structures do you want to generate ?
 If you have used an alignment that were highly similar it is sufficient to generate 1 structure. If you have used
approximate constraints or a template with very low similarity, multiple templates (you can generate just 1 structure, if it fails then generate more models) specify 20-50 structures.  If you specify more than 1 structure then you may be asked to specify a random seed number (must be an odd number).

Enter how many cycles of SECODG do you want to run (1 if no SECODG) ?
This option will not have any meaning if you generate only one structure. If you generate multiple structure and have used approximate constraints you can run multiple cycles of DIAMOD.