Oh, thank you ))) this molecule has 3 important flexible bounds and the
geometry is almost excellent for am1-bcc calculations. thank you for reply!
2011/10/4 David Case <dacase.rci.rutgers.edu>
>
>
> On Oct 3, 2011, at 5:20 PM, Алексей Раевский <rayevsky85.gmail.com> wrote:
>
> > Ok, thank you, but i don't understand if I have to minimize (optimize)
> > ligand structure and in what params before antechamber usage, or not?
> > whether a ligand conformation will have an effect on prmtop content or
> not?
> >
> The "bcc" charge model automatically optimizes the ligand geometry using
> the am1 Hamiltonian. If you are using RESP or other procedures you probably
> need to optimize yourself, and perhaps also select multiple conformations
> for floppy molecules. Look for examples at the RED web site.
>
> Note that the bcc model just finds the nearest local minimum conformation,
> so you should start with a fairly good geometry. This simple, automated,
> procedure is appropriate for relatively rigid molecules (where
> conformational sampling is not crucial) or for use on large numbers of
> ligands (where there might not be any good alternatives).
>
> ....good luck...dac
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Received on Tue Oct 04 2011 - 00:30:03 PDT
