[gmx-users] g_dih calculation doubt

Justin Lemkul jalemkul at vt.edu
Wed Dec 26 16:31:04 CET 2012

On 12/26/12 12:57 AM, Kavyashree M wrote:
> Dear users,
> I was using g_dih to find the phi/psi transitions of a protein
> along the trajectory using the following command -
> g_dih -f a.xtc -s a.tpr -o dihout.out -b x -e y -w
> When it started running it indicated many of the following lines
> "Dihedral around 7793,7804 not found in topology. Using mult=3"
> what does it mean..? they are not nearby atoms so as to calculate
> dihedral angle..

Clearly g_dih thinks they are.  Refer to your coordinate or topology files to 
find out what those atoms are.  A difference of only 11 atoms is not very large. 
  They could indeed be in the same residue or in a disulfide.

> At the end it gave the dihedral transitions of each residue along the
> trajectory - it displayed -
> "Calculated all dihedrals, now analysing..."
> and then it took backup of all residue transitions creating new
> xvg files of the same residues. I compared the two files ie, the
> backup file and the corresponding new file there was drastic differences
> why is there difference between these two files although both are
> plots of degrees v/s time.

Backup files are generated after multiple invocations of a command.  Apparently 
whatever you ran multiple times produced different output.

> One more question is some times it shows dihedral values of  more
> than 360.. sometimes 1000 etc.. does it mean that the bond has undergone
> rotation so many times.. I am sorry  I am not getting this. Also the file
> that it generates does not say which is phi/psi specifically. So I suppose
> 2nd column is phi and 3rd column is psi? it it right?

You'll have to provide snippets of your output, with complete .xvg header 
information here.  Most files are very well labeled so as to make the columns 



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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