## apbs-users

 [Apbs-users] Charge Density and Tutorial From: Paula Petrone - 2004-09-20 07:46:12 ```Hi all. I am beginning to use APBS and got stuck analising the charge density example of the tutorial (dna) However, I think my question goes further than that into the charge density distribution http://agave.wustl.edu/apbs/doc/html/tutorial/x349.html When I load the dna.pqr and run apbs it tells me that the net charge: Net charge -6.98e+01 e However, the calculated qdens.dx is never negative! I would expect some negative charge inside the dna, even if it is screened by layers of salt. If I do not put salt, (I set salt concentration to zero), then the qdens.dx gives me zero everywhere. (when I know that there is a net charge) I am puzzled. Where did the charge go? I would appreciate anyone that can drop a hint to this mistery. Thanks a lot! Paula Paula Petrone Biophysics Graduate Student Paula Petrone Biophysics Graduate Student _______________________________ Pande Group Clark Center, MC 5447 Stanford University Stanford, CA 94305-5447 Email: ppetrone@... _______________________________ ```
 Re: [Apbs-users] Charge Density and Tutorial From: Nathan A. Baker - 2004-09-20 12:46:31 ```Hi Paula -- The documentation probably isn't clear: the charge density is simply the mobile charge density and does not include macromolecular charges. Hope this helps. -- Nathan Paula Petrone (09-19-2004 22:45:28-0700): >Hi all. >I am beginning to use APBS and got stuck analising the charge density >example of the tutorial (dna) >However, I think my question goes further than that into the charge >density distribution > >http://agave.wustl.edu/apbs/doc/html/tutorial/x349.html > >When I load the dna.pqr and run apbs it tells me that the net charge: > >Net charge -6.98e+01 e > >However, the calculated qdens.dx is never negative! > >I would expect some negative charge inside the dna, even if it is >screened by layers of salt. > >If I do not put salt, (I set salt concentration to zero), then the >qdens.dx gives me zero everywhere. (when I know that there is a net >charge) > >I am puzzled. Where did the charge go? >I would appreciate anyone that can drop a hint to this mistery. > >Thanks a lot! >Paula > > >Paula Petrone >Biophysics Graduate Student > > >Paula Petrone >Biophysics Graduate Student > >_______________________________ >Pande Group >Clark Center, MC 5447 >Stanford University >Stanford, CA 94305-5447 >Email: ppetrone@... >_______________________________ > >_______________________________________________ >apbs-users mailing list >apbs-users@... >http://cholla.wustl.edu/mailman/listinfo/apbs-users End of message from Paula Petrone. -- Nathan A. Baker, Assistant Professor Washington University in St. Louis School of Medicine Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology 700 S. Euclid Ave., Campus Box 8036, St. Louis, MO 63110 Phone: (314) 362-2040, Fax: (314) 362-0234 URL: http://www.biochem.wustl.edu/~baker PGP key: http://cholla.wustl.edu/~baker/pubkey.asc ```