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 <[email protected]>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 <[email protected]> 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> > > > > ==============================**========== > > > > -- > > gmx-users mailing list [email protected] > > http://lists.gromacs.org/**mailman/listinfo/gmx-users< > http://lists.gromacs.org/mailman/listinfo/gmx-users> > > * Please search the archive at http://www.gromacs.org/** > > Support/Mailing_Lists/Search< > http://www.gromacs.org/Support/Mailing_Lists/Search>before posting! > > * Please don't post (un)subscribe requests to the list. Use the www > > interface or send it to [email protected]. > > * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists< > http://www.gromacs.org/Support/Mailing_Lists> > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
