extract a PDB from Gromacs TPR files

Extracts structure data from a Gromacs TPR file and outputs it to PDB format.

%% TPR2PDB.m
%
% Gromacs is useful for simulating all-atom systems, and it initiates these
% simulations with a TPR file. All TPR files contain coordinate data to
% initiate the simulation. Occasionally it is useful to open and check that
% structure. This program extracts it and converts it to PDB format for
% convenient viewing. The information extracted is coordinates, atom type,
% and partial charges. Partial charges are stored in the beta-factor column
% of the output file.
%
%
% ----- Requirements -----
%
% GROMACS
% This program uses the Gromacs command 'GMXdump' to create a text
% file. This avoids any problems that may precipitate from Gromacs
% updates and version changes. Be sure this command is in a valid
% path.
%
% gmxdump
% See above. The command that initiates this file is
% $> gmxdump -s [TPR file] > textForAnalysis.txt
% This program fails if this can't be done properly. Note that this
% is a Unix system command style, and may have issues when run with
% Windows. Use Putty or cygwin wrappers if using Windows. MatLab can
% be initiated from these wrappers.
%
% TPR file
% This is necessary. These are the files used to prepare Gromacs
% simulations.
%
%
% ----- Inputs -----
% TPR file (required)
% intermediate text file (optional, output of GMXdump)
%
%
% ----- Examples -----
% TPR2PDB('3IJU.tpr') % outputs coordinates to '3IJU.pdb'