[gmx-users] g_dih calculation doubt

[Kavyashree M]

Thanks both of you for the suggestions.
Regarding the backup files - I did not run the command
multiple times.

Thank you
kavya

On Thu, Dec 27, 2012 at 1:01 AM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> 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.
>
> Mark
>
> 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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