CCL: AM1-BCC charges in Antechamber



 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  <jimkress35|*|gmail.com>
 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