Re: [ccp4bb] X-PLOR
Thanks Francisco. Nicolas, thanks also for your feedback. In fact, I had already downloaded the X-PLOR manual, but I needed some more details on the H-atoms optimization procedure. That was for the purpose of a teaching work on a 1995 paper. Best regards, Nadir Pr. Nadir T. Mrabet Structural Molecular Biochemistry INSERM U-954 Nancy University, School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-les-Nancy Cedex France Phone: +33 (0)3.83.68.32.73 Fax: +33 (0)3.83.68.32.79 E-mail: Nadir.Mrabetat medecine.uhp-nancy.fr On 27/04/2012 16:59, Francisco Hernandez-Guzman wrote: Nadir, There is an explicit bulletin board for questions regarding CNS and XPLOR. I would suggest posting your question there. http://tech.dir.groups.yahoo.com/group/cnsbb/ Cheers, Francisco -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Nadir T. Mrabet Sent: Friday, April 27, 2012 6:34 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] X-PLOR Hi, Could someone explain to me the scientific details of the protocols used in X-PLOR to (1) build explicit hydrogen atoms onto X-ray structures and (2) optimize their positions? Many thanks in advance. Greetings, Nadir
Re: [ccp4bb] X-PLOR
Hi, I find some information here : http://www.csb.yale.edu/userguides/datamanip/xplor/xplorman/htmlman.html And for a more usefull answer, they explain that : The hbuild statement tries to build the position of any selected hydrogen based on the position of the heavy atom antecedents (Brünger and Karplus 1988). It works in a general way and can be used with any empirical force field. It performs local energy minimization in cases where the placement of the hydrogens is not unique. Waters close to the macromolecule are placed first, followed by waters that are farther away. Several iterations can be carried out to reach self-consistency. The minimization uses the energy function (Eq. 4.1 http://www.csb.yale.edu/userguides/datamanip/xplor/xplorman/node113.html#eqetotal) except that the specification of constraints interaction statements (Section 4.7 http://www.csb.yale.edu/userguides/datamanip/xplor/xplorman/node131.html#constraintsinteraction) are ignored. The hydrogen building facility does not use the improper or dihedral information in the topology file (Section 3.1.1 http://www.csb.yale.edu/userguides/datamanip/xplor/xplorman/node46.html#topologystatement). The chirality of methyl and methylene groups is determined by the order of four substituents to the central carbon atom as specified in the molecular structure. By changing the order in which the atoms are defined in the residue statement (Section 3.1.1 http://www.csb.yale.edu/userguides/datamanip/xplor/xplorman/node46.html#topologystatement), the chirality of the center is changed. Hydrogens are recognized by X-PLOR by their mass. All atoms with a mass less than 3.5 amu are considered hydrogens. Certain simulated annealing protocols (e.g., Section 20.3.3 http://www.csb.yale.edu/userguides/datamanip/xplor/xplorman/node395.html#dgsaprotocol) make use of artifically increased masses. If hydrogen building is employed in these protocols, the hydrogen building routine will return an error statement. In this case the user has to reset the mass of the hydrogen atoms to their physical values. To save CPU time, it is suggested to carry out the hydrogen building without nonbonded energy terms. The coordinates then will need minimization to relieve possible bad contacts between the initial hydrogen placements. You can find more information about the CHARMM force field apllied to the Explicit polar hydrogens of Nucleics acids and proteins HTH Nicolas Le 27/04/12 15:34, Nadir T. Mrabet a écrit : Hi, Could someone explain to me the scientific details of the protocols used in X-PLOR to (1) build explicit hydrogen atoms onto X-ray structures and (2) optimize their positions? Many thanks in advance. Greetings, Nadir
[ccp4bb] X-PLOR
Hi, Could someone explain to me the scientific details of the protocols used in X-PLOR to (1) build explicit hydrogen atoms onto X-ray structures and (2) optimize their positions? Many thanks in advance. Greetings, Nadir -- Pr. Nadir T. Mrabet Structural Molecular Biochemistry INSERM U-954 Nancy University, School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-les-Nancy Cedex France Phone: +33 (0)3.83.68.32.73 Fax: +33 (0)3.83.68.32.79 E-mail: Nadir.Mrabetat medecine.uhp-nancy.fr
Re: [ccp4bb] X-PLOR
Nadir, There is an explicit bulletin board for questions regarding CNS and XPLOR. I would suggest posting your question there. http://tech.dir.groups.yahoo.com/group/cnsbb/ Cheers, Francisco -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Nadir T. Mrabet Sent: Friday, April 27, 2012 6:34 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] X-PLOR Hi, Could someone explain to me the scientific details of the protocols used in X-PLOR to (1) build explicit hydrogen atoms onto X-ray structures and (2) optimize their positions? Many thanks in advance. Greetings, Nadir -- Pr. Nadir T. Mrabet Structural Molecular Biochemistry INSERM U-954 Nancy University, School of Medicine 9, Avenue de la Foret de Haye, BP 184 54505 Vandoeuvre-les-Nancy Cedex France Phone: +33 (0)3.83.68.32.73 Fax: +33 (0)3.83.68.32.79 E-mail: Nadir.Mrabetat medecine.uhp-nancy.fr
