On Sun, Sep 10, 2017, Zachary Smithline wrote:
>
> 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: Unable to achieve self consistency to the tolerances specified
It can be difficult to get convergence on highly charged polyphosphate
complexes. You could see if charges are already available in the R.E.D.
database, or if you can use their software to get new resp charges.
You should also consult Notes 6 and 7 in Section 15.2 of the Amber 2017
Reference Manual.
>
>
> 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?
No.
>
> 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?
Get charges for fragments (such as a nucleotide intended to be a part of a
polymer chain) is not as simple as it might be. You have to add a capping
group at the 5' end, run antechamber on an entire molecule (with integer
charge), then remove the capping group. This is outlined for proteins in
tutorial B5. You'll have to use this understand the general procedure, but
then modify things because (1) you have RNA rather than protein; (B) you
want a residue (as I understand it) that is just connected on one end (the 5'
end), and not on the other.
...good luck....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Sep 11 2017 - 05:30:04 PDT
