Dear David, The peptide is having a -ve charge of 3. Though the components might dependent upon the orientation but the average might be the same irrespective of the orientation I suppose.
Ram. On Tue, Mar 17, 2009 at 3:54 AM, David van der Spoel <[email protected]>wrote: > rams rams wrote: > >> Dear Users, >> >> I am trying to obtain the dipole moment of a 40 amino acid residue peptide >> using g_dipoles. I am getting a huge number (about 700 Debye). I expect it >> to be around 150 Debye (based on other studies). To make sure it I extracted >> a shapshot of the structure and obtained the dipolemoment using the >> following command: >> >> g_dipoles -f ab42_1.0_30ns.pdb -s MD_ab42.tpr -o Mtot.xvg -n prot_dip.ndx >> >> I am giving the last few lines of the output below: >> >> Dipole moment (Debye) >> --------------------- >> Average = 516.7213 Std. Dev. = 0.0000 Error = 0.0000 >> >> The following averages for the complete trajectory have been calculated: >> >> Total < M_x > = -54.3459 Debye >> Total < M_y > = 12.8373 Debye >> Total < M_z > = 513.695 Debye >> >> Total < M_x^2 > = 2953.47 Debye^2 >> Total < M_y^2 > = 164.796 Debye^2 >> Total < M_z^2 > = 263883 Debye^2 >> >> Total < |M|^2 > = 267001 Debye^2 >> Total < |M| >^2 = 267001 Debye^2 >> >> < |M|^2 > - < |M| >^2 = 0 Debye^2 >> >> Finite system Kirkwood g factor G_k = 0 >> Infinite system Kirkwood g factor g_k = 0 >> >> Epsilon = 1 >> >> The same structure (i.e., what i have used in the above command) if I open >> and check for the dipole moment using YASARA suite of program it is showing >> as 173 Debye. Which is reasonable. Am I making any mistake while obtaining >> the dipole moment using g_dipoles or I am looking at the wrong file ?? >> > > Is the peptide neutral? Otherwise the result might be orientation > dependent. > > > >> Thanks. >> >> Ram. >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >> > > > -- > David van der Spoel, Ph.D., Professor of Biology > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. > [email protected] [email protected] http://folding.bmc.uu.se > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >
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