GPMAW is installed on Windows in the Program Files\gpmaw\ directory. Here is installed the main executable ‘gpmaw3.exe’ along with the help file ‘gpmaw.chm’ along with a couple of minor non-essential programs. BLAST, ClustalW and XTandem are installed in subdirectories and will be called directly from GPMAW. A sub-directory ‘documents’ contains pdf-versions of the user manual and the introductory ‘Dummies guide’. These files can be called from GPMAW in the ‘Help’ menu.

Essential user-accessible files are created in the individual users Document section, e.g. \Users\<username>\Documents\GPMAW\

Here the essential ini-file ‘gpmaw.ini’ is located which contain all start-up information and the program will update it during each run and upon close-down. If there are multiple users of the computer, each will have their own user-file structure in their private Documents section.

If the file is deleted, GPMAW will recreate it, but some information will likely be lost.

A subdirectory called ‘user’ is where user-files will be stored, typically sequence files. Upon installation, two demonstration sequences ‘Blood.seq’ and ‘insulin.seq’ will be present. When a sequence file is updated by GPMAW, the old version will be renamed with the extension ‘.bak’.

Another subdirectory ‘system’ is created containing essential system files. In particular a number of mass files are installed:
‘AA_MASS.mss’ is the default mass file containing information on amino acid residues, abbreviations, and compositions. A number of additional mass file are included, mainly for quickly changing the default mass of cysteine upon alkylation (e.g. acetamid.mss, ae.cys.mss, cys_acid.mss). Other mass files can be generated by the user in the program and stored here.
Another essential file type is the modification file (.MOD). These contain the composition of modifications along with valid residues. The default modification files are  ‘ADDUCTS.MOD’ and ‘FixedModif.MOD’. These can be freely modified, added to and saved under different names by the user through the program, but should always be located in the ‘system’ directory.

A special version of the MOD file is ‘Terminal.tms’ which contains the composition of the N- and C-termini. This file can be changed but should always have the same name.

‘Unimod.xml’ is an xml formatted file containing a large amino acid modification database maintained by Matrix Science and updated versions can be downloaded from here.

Finally the file ‘Xlinker.rea’ is a file containing names and compositions of chemical cross-linkers used for related functions in GPMAW.

Site last updated: February 04, 2025