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 Mon Oct 03 2011 - 17:00:02 PDT
