GPMAW is by default installed on Windows in the Program Files\gpmaw\ directory. Here is installed the main executable ‘gpmaw3.exe’ and 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\. This happens during installation, but you can change the location for special purposes, see below.

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.

Changing the location of GPMAW user files:

For certain situations like multiple users or virtual environments you may not always have access to named user directory. In this case the user must open GPMAW and select Setup System and the panel called ‘Directories’. Click on the ‘Change file admin’ button, and in the dialog you can change to a shared directory. The ini file and all files in the system and user directories will be copied along too. Shut down GPMAW to fully update the ini file and upon restart, you should be in shared mode.

for the Inline mode you need to set inline parameters and copy the relevant files and directories manually, please consult the online help and manual.

How does GPMAW differentiate the different start modes?

Upon startup, GPMAW initially checks the presence of inline parameters, and if the ‘/U:’ parameter is present the specified .ini file is loaded. If not, the shared files Documents directory is checked for gpmaw.ini and finally the personal Documents directory.

Upon installation, the personal Documents directory is used, as this will be the choice for the majority of users.

Site last updated: February 14, 2025