Thread: [Apbs-users] angle between water and field line
Biomolecular electrostatics software
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From: Kay G. <kay...@ph...> - 2006-05-05 10:28:45
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Hi there, I want to calculate the angle between a water dipole and the field line of a protein. Any idea how I might do that? Thanks, Kay. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kay-Eberhard Gottschalk Applied Physics and Center for Nano Sciences Ludwig-Maximilians University Amalienstr. 54 80799 Munich, Germany Phone: +49-89-2180 3436 |
From: Nathan B. <nat...@wu...> - 2006-05-05 13:20:53
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It shouldn't be too hard. First, I would calculate the potential *in the absence of the water molecule* and save the result as an OpenDX file. Next, you can load this OpenDX data into a Vgrid object either using the template code in apbs/tools/mesh/value.c or through Todd's apbs/tools/python/vgrid/vgrid.py (assuming you compiled Python support into APBS). Finally, you can use the Vgrid object to evaluate the field at specific points in space (e.g., the location of your water dipole).=20 This is demonstrated in the apbs/tools/mesh/value.c template code and should be a reasonable starting point for your calculations. Please let us know if you have any questions. Thanks, Nathan On 5/5/06, Kay Gottschalk <kay...@ph...> wrote: > Hi there, > > I want to calculate the angle between a water dipole and the field > line of a protein. Any idea how I might do that? > Thanks, > Kay. > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Dr. Kay-Eberhard Gottschalk > Applied Physics and Center for Nano Sciences > Ludwig-Maximilians University > Amalienstr. 54 > 80799 Munich, Germany > > Phone: +49-89-2180 3436 > > > > > > ------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job ea= sier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronim= o > http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&dat= =3D121642 > _______________________________________________ > apbs-users mailing list > apb...@li... > https://lists.sourceforge.net/lists/listinfo/apbs-users > > -- Assistant Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ |