Re: [ccp4bb] APBS

[Boaz Shaanan]

Hi, The best place to pose this question would be the APBS bb which you can  join from this site: http://www.poissonboltzmann.org/apbs/ You may also check the FAQ there, maybe your question (+ an answer) would be there already.   Cheers,            Boaz   Boaz Shaanan, Ph.D.                                         Dept. of Life Sciences                                      Ben-Gurion University of the Negev                          Beer-Sheva 84105                                            Israel                                                                                                                  E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220  Skype: boaz.shaanan                  Fax:   972-8-647-2992 or 972-8-646-1710                          From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Reginald McNulty [rmcnu...@uci.edu] Sent: Tuesday, July 05, 2011 8:24 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] APBS Dear CCP4BB, I apologize for the off topic question. I have determined the 3D structure of a membrane protein transporter and want to make a figure showing the surface charge. So, I ran PDB2PQR and specified pH 5.4. I understand the next step is to run APBS. I know there are different dielectric constants for parts of the protein exposed to membrane and  cytosolic  portions. I'm wondering if I need to take this into account when generating a figure for surface charge? If so, I'm wondering how do I tell the program residues that are embedded in the membrane and those that are not? If you could help me answer these questions or point me in the right direction I'd greatly appreciate it. Best regards, Reggie McNulty Department of Molecular Biology and Biochemistry UC Irvine