Output of MPACK

The output files will be changed in the higher version. So please refer to this section for any changes. If the core file name given is ‘XXXX’ then the following output files will be produced.

Let the following be the input files:

align1.aln (alignment file)
align1.pdb (template co-ordinate file)

Out put files:

XXXXMPACK.LOG (LOG file containing details of program execution, MOLMOL scripts)
XXXX_Yex.aln         (Reformatted alignment file, for the 1st alignment ie master align Y=1)
alignYre.pdb            (Renumbered pdb file to be used for MOLMOL, Y corresponds to the align)
XXXXexdisrun.sh    (Script to run exdis, only for the master alignment)
XXXXex.aco             (Angle constraint file)
XXXXex.upl              (upper limit file)
XXXXex.lol               (lower limit file)
XXXXex.ang            (approximate starting structure for DIAMOD )
XXXXdia.min           (minimization file for DIAMOD)
XXXXdiarun.sh       (Script to execute DIAMOD)
XXXXdiaY.clol         (Corrected lower limit file valid if you use SECODG > 1 option, Y is the round)
XXXXdiaY.cupl        (Corrected upper limit file valid if you use SECODG > 1 option, Y is the round)
XXXXdiaY.lol            (modified lower limit file in round Y)
XXXXdiaY.lol            (modified upperl limit file in round Y)
XXXXdiaY.ovw        (Overview file containing target function for the round Y)
XXXXdiaY.res          ( Result, minimization details of DIAMOD cycle run Y)
XXXXdiaYZZZ.cor   (DG coordinate file for the model number ZZZ  generated in cycle Y)
XXXXdiaYZZZ.ang  (ANG file for the model number ZZZ generated in the cycle Y)
Mscr_targ.seq          (FASTA format of target sequence)

Selecting crude model for energy minimization:

If you have selected to generate 1 model then visualize it to see whether any mirror images, energetically impossible loopings or crossings, complex meaningless topologies are present. If you so generate more models by specifying suitable option or edit *diarun.sh file to generate more models and rerun it. If you have already generated more models, then check the file *dia.ovw to find the model with the least target function. Use this as the starting structure for FANTOM minimization.  Currently fantom minimization is not included in the MPACK. One must create fantom minimization files or alternatively use perl script fantomminimize.pl that is supplied with the package. Finally to run energy minimization you must execute fan_run.sh that is created by fantomminimize.pl. You must monitor the output structure written at different stages of minimization. For a good model the conformational energy must be negative and the gradient should be close to ‘0’.