Does chimera allow you to define the force-field? I'm concentrating on using PARSE for most of my work. Also, I like how PDB2PQR uses proPKA as the model for predicting pKa values in the charge calculation. Does Chimera share this functionality? Thank you, Nikolay Rodionov -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Friday, April 20, 2012 9:13 AM To: Nikolay Igorovich Rodionov Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] Charge calculations PDB2PQR Hi Nikolay, Well, Chimera itself does charge assignments, see the Add Charge tool (in Chimera menu under Tools... Structure Editing). It uses a lookup table for standard residues and Antechamber to calculate charges for other residues, as explained in the manual page: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/addcharge...> However, Chimera does not write out the PQR format, it only reads it. I can't answer anything specific about the PDB2PQR server...it's not part of Chimera and I haven't used it very much. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Apr 20, 2012, at 7:53 AM, Nikolay Igorovich Rodionov wrote:
Hi all, Does anyone knows any alternative charge calculating software packages to PDB2PQR. I need to calculate partial charge distribution but the local copy of PDB2PQR that I installed has some kind of glitch where it is scrapping all of the water molecules from my solvated protein while doing the analysis. I think it has something to do with the side of my PDB file since I am using about 30K atoms, at least, and everything goes perfectly when I work with less 10K atoms. So, I guess the second question is, has anyone else ever encountered this problem? Sincerely, Nikolay Rodionov