[gmx-users] g_dih calculation doubt

Kavyashree M hmkvsri at gmail.com
Wed Dec 26 06:57:06 CET 2012

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..

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.

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?

Thank you

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