VMD-L Mailing List

From: Hamid (hamid592004m_at_yahoo.com)
Date: Fri Dec 06 2013 - 13:42:53 CST

Dear Alexandre for Hbond criteria, cut off angle must set to 30 degree (or 150 degree) and cut off distance set to 3.5 Ang. Hamid Mosaddeghi PhD of Physical Chemistry On Friday, 6 December 2013, 14:26, Norman Geist <norman.geist_at_uni-greifswald.de> wrote: Yes, but I was just talking about the VMD plugin. The problem why this hasn’t still been implemented might be, that without a movement of the atoms, means cross-frame measurements, this energy hbond detection might be less accurate here or just hard to implement, whereas with the current implementation a hbond can easily be visualized for one single point in time, so also for a pdb from the database and probably therefore is the better choice for most people. Of course, if someone chooses hbonds to be a main topic of the own work, this is another thing and one should implement an own analysation.   Norman Geist.   Von:lloyd riggs [mailto:lloyd.riggs_at_gmx.ch] Gesendet: Donnerstag, 5. Dezember 2013 22:11 An: Norman Geist Betreff: Aw: AW: vmd-l: hydrogen bond criteria   The IUPAC redefined hydrogen bond definitions in 2011.  There is now really no set angle/distance rather energy of the bonds due to x-ray structures and dynamics.  Thus these need to be looked at (for the software) say by user defined shells or parmeters based on what you wish to observe.  This is just my thoughts based on defining them now as energy based rather than pre-set angles and distances, which was dated back to the early years of chemistry (1880-1940).   Stephan Watkins, PhD   Gesendet: Donnerstag, 05. Dezember 2013 um 14:10 Uhr Von: "Norman Geist" <norman.geist_at_uni-greifswald.de> An: "'Alexandre PERRET'" <alexandre.perret_at_etudiant.univ-reims.fr> Cc: "VMD Mailing List" <vmd-l_at_ks.uiuc.edu> Betreff: AW: vmd-l: hydrogen bond criteria The angle already is defined as A-D-H and an ideal hbond would have angle 0.   Norman Geist.   Von:owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] Im Auftrag von Alexandre PERRET Gesendet: Donnerstag, 5. Dezember 2013 11:32 An: vmd-l_at_ks.uiuc.edu Betreff: vmd-l: hydrogen bond criteria   Hello VMD users,   I found something a bit odd using the hbonds plugin. According to the plugin, the criteria for the formation of a hydrogen bond are the distance between the donor D and the acceptor A and the angle D-H-A. The cut-off angle is by default 20 degrees, which means that D and A are too close to each other. In my opinion, it should be the angle H-D-A with a cut-off angle of 20 degrees. What do you think ?   Thank you in advance, Alex   -- Alexandre Perret PhD Student Groupe de Spectrométrie Moléculaire et Atmosphérique - UMR CNRS 7331 Université Reims Champagne-Ardenne Campus Moulin de la Housse - BP 1039 51687 REIMS FRANCE alexandre.perret_at_etudiant.univ-reims.fr Tél : (+33/0) 3 26 91 33 66 Fax: (+33/0) 3 26 91 31 47       ________________________________ Diese E-Mail ist frei von Viren und Malware, denn der avast! Antivirus Schutz ist aktiv.   ________________________________ Diese E-Mail ist frei von Viren und Malware, denn der avast! Antivirus Schutz ist aktiv.