[gmx-users] g_dih calculation doubt

[Justin Lemkul]

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

-- 
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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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