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Hello Andrea-- > > > >> I am using vmd-xplor to calculate the E[NOE] as reported in > >> http://www.cell.com/biophysj/abstract/S0006-3495(06)71992-0 paper. > >> the file.tbl is read properly and everything goes fine. I do: > >> noe load 0 0 file.tbl > >> noe calc > >> and a series of violations are reported. Then, in the tcl console I > >> get a number (i.e. 6.23) and I think that this is the E[NOE]. Is it > >> right? > > > > That should be the noe cost. > > > >> If so, what kind of unit is it? kcal/mol or kj/mol? > >> > > > > kcal/mol. Note, that the graphical interface should be more intuitive. > > > > if the value is the NOE cost, it should depend on the cutoff used. > However, this value does not change in function of the cutoff, even > for higher cutoff, when not violations are found. > > how is it possible? I think you are still referring to VMD-XPLOR, and the cutoff value in the GUI there (the same as the threshold value in Xplor-NIH) serves only to determine whether a restraint is violated- it does not affect the energy calculation. best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.9 <http://mailcrypt.sourceforge.net/> iEYEARECAAYFAkvkIn4ACgkQPK2zrJwS/lYN5wCeIPnoSTAPZ1rMv+03VWIyFiHV LtAAn3ceWuIsy/ZA0YiMM+gFxA47neOg =ej+8 -----END PGP SIGNATURE-----
