I think everyone will tell you that using the Mulliken charges is not
an appropriate practice in classical MD, since your electrostatics
will be totally unrealistic.
It is difficult to judge why hydrogens collapse onto oxygens without
the particular snapshots. Perhaps, there is some erratum in angles or
dihedrals for these atoms?
Dr. Vitaly V. Chaban, 430 Hutchison Hall
Dept. Chemistry, University of Rochester
120 Trustee Road, Rochester, NY 14627-0216
THE UNITED STATES OF AMERICA
On Thu, Jul 12, 2012 at 6:23 PM, Maria Minakova
<mariabiophysics.gmail.com> wrote:
> Hello,
>
> I am minimizing a complex synthetic compound, which also has phosphonic acid groups attached to it:
> OH
> |
> R - P = O
> |
> OH
> The automatic atom type assignment (gaff) put (py) atom type for central P, (o) for double bond O, (oh) for O in OH fragment, and (ho) for H in OH fragment.
> I did not put any restrictions for minimization, and within fist 1000 steps hydrogens collapsed onto neighboring oxygens, which is not supposed to happen.
> I wonder if there is something wrong with my parametrization or minimization script.
> Any ideas or suggestions?..
>
> additional info:
> Partial charges were assigned by mulliken method (resp didn't work well with the rest of this compound).
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jul 12 2012 - 16:30:03 PDT
