[gmx-users] Re: g_dih

[Graham Smith]

> I was using g_dih and could not get any output. The program asked me
> for the number of frames. According to the Diagnostics of the
> on-line manual it should not. Is there a way to fix the problem? 

If you're using it with a trajectory just give the number of frames
and it'll work anyway 

g_dih -s sim.tpr -f sim.xtc -o dihed.out

creates a file for every residue and dihed.out will be empty 

g_dih -s sim.tpr -f sim.xtc -o dihed.out -sa 

suppresses the files for every residue but does "cluster analysis in
dihedral space" which is output in dihed.out (but unless your protein
is very short, or your traj is very long, every frame is likely to be
different). The output is a string of numbers which seems to specify
the current "dihedral bin" for each residue. 

If you want it to evaluate a single configuration and do 

g_dih -s sim.tpr -f conf.pdb -o dihed.out [-sa]
I can't get any output either. It seems to need at least 2 config
frames, of which only one is used. An ugly workround is 
trjconv -f conf.pdb -o temp.xtc 
trjconv -f conf.pdb -o temp.xtc -app 
g_dih -s sim.tpr -f temp.xtc -o dihed.out [-sa]

despite its name I think g_dih does only phi and psi. 

If you want other dihedrals you need g_chi (which, despite *its* name,
can do phi and psi as well). 

e.g. 
g_chi -phi -psi -maxchi 2 -all -g chi.log -c sim.tpr -f sim.xtc 

+many other options 

(run g_chi in a separate directory as most combinations of options
cause it to produce millions of files, e.g -all causes a file for each
residue and each dihedral to be output). 

HTH 

Graham 

########################################################################

Dr. Graham R. Smith, 		       Department of Biological Sciences,  
Biomolecular Modelling Laboratory,     Biochemistry Building,              	
Cancer Research UK, 		       Imperial College of Science,        	
44 Lincoln's Inn Fields, 	        Technology & Medicine,             	
London WC2A 3PX,		       London SW7 2AZ,                     	
U.K. 				       U.K.                                	
Tel: +44-(0)20 7269 3348 	       Tel: +44-(0)20 7594 5737            	
email: graham.smith at cancer.org.uk	
URL: http://www.bmm.icnet.uk/~smithgr