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 University