Dear All,
Does anybody have a lot of experience deriving AM1-BCC charges quickly in
Antechamber? I am trying to parameterize charges for: 3'-end 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. In both
cases, the error is of the form (from the tail of the sqm.out file):
QMMM: ERROR!
QMMM: Unable to achieve self consistency to the tolerances specified
QMMM: No convergence in SCF after 1000 steps.
QMMM: E = -0.1131E+07 DeltaE = -0.7500E+01 DeltaP = 0.6037E-01
QMMM: Smallest DeltaE = 0.1146E-06 DeltaP = 0.2870E-04 Step = 98
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'-end adenine nucleotide with its 3'O deprotonated, I don't think
antechamber will take a non-integer charge. Can I use the same strategy,
meaning: just set the charge to an integer, then scale the charges? If
not, does anybody have a suggestion for how to deal with these problems? Is
there any simple way to do these tasks in Antechamber?
Many thanks,
Zachary Smithline
Lab of Thomas Steitz
Departments of MB&B and Chemistry
Yale University
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Sep 10 2017 - 00:00:02 PDT
