Thread: [Apbs-users] coulombic component
Biomolecular electrostatics software
Brought to you by:
sobolevnrm
From: Madhumalar A. <mad...@bi...> - 2006-10-19 12:18:07
|
Dear users, I am looking at the binding energy for the formation of protein dimer, using APBS. The columbic component of one monomer, calculated using /usr/local/src/apbs-0.4.0/tools/manip/coulomb is -2.266186884093e+05 and the same thing, when calculated using sdie=pdie=2.0 is 3.028462044692E+05 does it mean that the selfenergies are not removed in the system? Thanks for any help. Madhu |
From: Nathan B. <nat...@ma...> - 2006-10-20 11:05:47
|
Hi Madhu -- You are correct: the APBS calculation does not remove self-energies; the coulomb calculation does remove self-energies. When solving the equation numerically through APBS, the self-energies must be removing through a reference calculation (e.g., in solvation/binding energy computation). Thanks, Nathan On Oct 19, 2006, at 7:17 AM, Madhumalar Arumugam wrote: > Dear users, > I am looking at the binding energy for the formation of protein > dimer, > using APBS. > The columbic component of one monomer, calculated using > /usr/local/src/apbs-0.4.0/tools/manip/coulomb is > > -2.266186884093e+05 > > and the same thing, when calculated using sdie=pdie=2.0 is > > 3.028462044692E+05 > > does it mean that the selfenergies are not removed in the system? > > > Thanks for any help. > Madhu > > > > > > ---------------------------------------------------------------------- > --- > 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 easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache > Geronimo > http://sel.as-us.falkag.net/sel? > cmd=lnk&kid=120709&bid=263057&dat=121642 > _______________________________________________ > 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/ |