On Mon, Jun 25, 2012, Jitesh Doshi wrote:
>
> I am preparing a ligand for MD Simulation using amber. I am also running
> Gaussian calculations on it. When I keep all the hydrogens in my ligand,
> Gaussian runs fine but I face a problem while importing my ligand pdb in
> tleap, saying Maximum coordination exceeded. when i fix this issue by using
> set command (set pert true), i face problem while saving the topology
> files.. This is happening to only non-polar hydrogens. So when I tried
> using my ligand with just polar hydrogens, now Gaussin calculation is not
> working that fine. Any help regarding the hydrogens in the ligand and
> mentioned problem is welcomed.
You need to be more specific. Look at your molecule (or the error messages)
to see what atoms are having too many bonds (max coordination). Saying "I
face [a] problem" (in using tleap) is no help at all: *what* problem did you
face?
Of course, with Gaussian or any other quantum chemistry package, you need to
have *all* the hydrogens present.
....dac
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Received on Mon Jun 25 2012 - 09:00:02 PDT
