Output of MPACKThe 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)
Out put files:XXXXMPACK.LOG (LOG file containing details of program execution, MOLMOL scripts)
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’.