All:
I am trying to generate charges for a modified nucleic base using
Antechamber and the RESP protocol. However, the charges are highly
exagerated. In many cases the charges are have changed sign from what is
found in the corresponding parm98 unit or in the mopac calculation for the
same molecule.
I'm getting methyl hydrogens having partial charges of -2.51!
Here are the steps I used to create this mess:
1) Created model in insight
2) Minimized using mopac interface in insight environment
3) "antechamber -i <input file> -fi mol2 -o <output> -fo gcrt"
4) Edited the output of antechamber to only run optimization, since, I was
having problems w/ Gaussian crashing. I basically ran the input through a
Gaussian (g98) minimization by changing the first link to:
UHF/6-31G* Test opt SCFCYC=256
5) Took the optimized output and ran a single point resp calculation with
first link being:
UHF/6-31G* Test SCF=Tight Pop=MK iop(6/33=2) iop(6/42=6)
which is basically the antechamber-generated file w/o the optimization.
6) Calculated charge w/ the following command.
antechamber -i <gaussian .out> -fi -gout -o <prep file> -fo -prepi
-c resp
7) Examined the prep file w/ xleap to discover the bad charges.
The problems seem to be most pronounced along a stretch of extended alkyl
chain. I remember in some of the papers that this can be a problem.
However, there are problems all over.
Could this be a units mismatch between Gaussian and amber? Gaussian is
working in Hartree-Bohr-Radians. I doubt it, but, need to mention it as a
possibility.
Received on Wed Oct 23 2002 - 14:50:56 PDT
