[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
Re: [ccp4bb] How to create electrostatic surface of modified DNA by APBS?
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
Re: [ccp4bb] How to create electrostatic surface of modified DNA by APBS?
Hi Xiaoming, I would download pdb2pqr 1.8 from the apbs website and install it. (linux) It can handle nucleic acid, (3 letter code) . After you installed it run it with python /whereeveritis/pdb2pqr-1.8/pdb2pqr.py -h it will print the options. Hope this helps. Fred [32m*** Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular BiologyFax: 301-496-0201 DHHS/NIH/NIDDK e-mail:fred.d...@nih.gov Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476...@mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred ***[m
