Re: [ccp4bb] How to create electrostatic surface of modified DNA by APBS?

[Boaz Shaanan]

Hi Xiaoming, I don't have the pdb2pqr manual in front of me right now. In cases where the pdb2pqr instructions don't address the problem that I faced I sent a message to their BB. They always came up with a solution. Just try to send them a message.      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: Xiaoming Ren [xiaomingre...@gmail.com] Sent: Thursday, April 24, 2014 11:06 PM To: בעז שאנן Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] How to create electrostatic surface of modified DNA by APBS? Hi Boaz: I tried running pdb2pqr server online, but it ended up with an error, saying "local variable 'key' referenced before assignment", which I don't know how to understand and handle with. Thanks, Xiaoming On Thu, Apr 24, 2014 at 3:59 PM, Boaz Shaanan <bshaa...@bgu.ac.il> wrote: Hi, It's pdb2pqr problem (unknown residue). I guess you ran pdb2pqr prior to running APBS, if not, you should. So, you should submit your question to either the APBS or pdb2pqr BB's. They are very helpful people.    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 Xiaoming Ren [xiaomingre...@gmail.com] Sent: Thursday, April 24, 2014 10:32 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] How to create electrostatic surface of modified DNA by APBS? Dear all: I'm having a problem create the electrostatic surface for a DNA chain containing several modified nucleotides. APBS could not identify those residues and reported them as unassigned. What should I do to solve this problem? Thanks a lot and best, Xiaoming