[gmx-users] g_dih calculation doubt

Mark Abraham mark.j.abraham at gmail.com
Wed Dec 26 20:31:12 CET 2012

Unfortunately, g_dih was written before 1997 and its documentation is very
poor. It does not actually read the connectivity in the .tpr file, nor does
it attempt to infer connectivity other than for some protein backbone
dihedrals. For some reason, it thinks it finds some for your topology, but
can't find parameters for them (wherever it imagines it should find them).

As far as I can see, its functionality is entirely duplicated by g_angle,
so g_dih will probably be removed in 4.6. I suggest you use g_angle for
whatever you are trying to do.


On Wed, Dec 26, 2012 at 4:31 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> ==============================**==========
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