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
obvious.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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