CCL: AM1-BCC charges in Antechamber

 Sent to CCL by: "Jim Kress" [jimkress35~!]
 Did you ask your question on the Amber mailing list?  I see these questions
 coming up quite frequently there.
 AMBER mailing list
 -----Original Message-----
 > From:|*|
 [|*|] On
 Behalf Of Zachary
 B Smithline zachary.smithline(0)
 Sent: Saturday, September 09, 2017 5:03 PM
 To: Kress, Jim  <jimkress35|*|>
 Subject: CCL: AM1-BCC charges in Antechamber
 Sent to CCL by: "Zachary B Smithline" [zachary.smithline]_[]
 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
 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
 Many thanks,
 Zach Smithline
 Lab of Thomas Steitz
 Departments of MB&B and Chemistry
 Yale University