From owner-chemistry@ccl.net Sat Sep 9 22:46:00 2017 From: "Jim Kress jimkress35:gmail.com" To: CCL Subject: CCL: AM1-BCC charges in Antechamber Message-Id: <-52980-170909224424-5543-sbJJxPxZM4NL584iqnWrsw-.-server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Sat, 9 Sep 2017 22:44:03 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [jimkress35~!~gmail.com] Did you ask your question on the Amber mailing list? I see these questions coming up quite frequently there. AMBER mailing list AMBER|*|ambermd.org http://lists.ambermd.org/mailman/listinfo/amber Jim -----Original Message----- > From: owner-chemistry+jimkress35==gmail.com|*|ccl.net [mailto:owner-chemistry+jimkress35==gmail.com|*|ccl.net] On Behalf Of Zachary B Smithline zachary.smithline(0)yale.edu Sent: Saturday, September 09, 2017 5:03 PM To: Kress, Jim Subject: CCL: AM1-BCC charges in Antechamber Sent to CCL by: "Zachary B Smithline" [zachary.smithline]_[yale.edu] Dear All, Does anybody have a lot of experience deriving AM1-BCC charges quickly in Antechamber? I am trying to parameterize charges for: 3' adenine nucleotide with its 3'O deprotonated (since the 3' terminal residues in Amber usually have -0.6921 charge, my residue should have -1.6921); pyrophosphate (charge -4); and dATP (charge -4). After generating .pdbs, I was trying to run the command: antechamber -i FILE_NAME.pdb -fi pdb -o FILE_NAME.mol2 -fo mol2 -c bcc -s 2 -nc CHARGE Both dATP and pyrophosphate give me errors when I use -nc -4; however, when I decrease the charge (say, to -2), the antechamber command works. Is it ok to assume the charge distributes uniformly as it is decreased, meaning: can I just double all my charges? For the 3' adenine nucleotide with its 3'O deprotonated, I don't think antechamber will take a non-integer charge. Can I use the same strategy, and just scale the charges? If not, does anybody have a suggestion as to how to deal with these problems? Is there any simple way to do these tasks in Antechamber? Many thanks, Zach Smithline Lab of Thomas Steitz Departments of MB&B and Chemistry Yale Universityhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt