Hi Charles, that's correct! In fact from your paper (Journal of Magnetic Resonance 149, 239?244 (2001))
E(noe) = k(Rcalc - Rmin)^2 so there is not cutoff contribution to the E(noe). sorry about that thanks a lot andrea On 05/07/2010 04:23 PM, Charles at Schwieters.org wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > > 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----- > -- ------------------------------- Andrea Spitaleri PhD Dulbecco Telethon Institute Center of Genomics, BioInformatics and BioStatistics c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) Tel: 0039-0226434348 Fax: 0039-0226434153 http://sites.google.com/site/andreaspitaleri/ http://www.linkedin.com/in/andreaspitaleri ------------------------------- ------------------------------------------------------------- DAI IL TUO 5 X MILLE AL SAN RAFFAELE. BASTA UNA FIRMA. SE FIRMI PER LA RICERCA SANITARIA DEL SAN RAFFAELE DI MILANO, FIRMI PER TUTTI. C.F. 03 06 42 80 153 INFO: 5permille at hsr.it - www.5xmille.org
