mdff

Usage: mdodelmaker mdff -pdb <input pdb file> -density <input density file> -res <resolution of density in Angstroms> ?options?
Options:
-workdir <working/project directory for job> (default: $DefaultMDFFWorkDir)
-jobname <name prefix for job> (default: taken from -model)
-fixed <atomselect text for fixed atoms> (default: $DefaultFixed)
-gscale <grid scaling factor for fitting forces> (default: $DefaultGScale)
-minsteps <number of minimization steps> (default: $DefaultMinSteps)
-numsteps <number of simulation steps> (default: $DefaultNumSteps)
-chseg <file containing lines of desired 'name' 'chain' 'segname'> (Default: from input pdb)
-topfiles <list of topology files to use>(Default: $DefaultTopFiles)
-parfiles <list of parameter files to use>(Default: $DefaultParFiles)
-dcdfreq <frequencey of dcd output>(Default: $DefaultDCDFreq)
-namdargs <arguments to pass to namd> (default: none)
-ss <secondary structure restraint file> (default: auto-generated)
-cis <cispeptide restraint file> (default: auto-generated)
-chir <chirality restraint file> (default: auto-generated)
-extrab <list of additional extrabonds files> (default: none)