Oh, another problem that is coming up...
If a molecule has a charge (-1), can antechamber treat it correctly?
David
On Thu, Jun 30, 2011 at 2:38 PM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> David,
>
> > Another thing we've done is optimized and calculated the energy and
> charges
> > of the Ser-PPP resiude in Gamess.
>
> With R.E.D. Server, you can use Gaussian 2003, Gaussian 2009,
> Gamess-US or Firefly.
>
> > But then how do I make the mol2 file and frcmod files?
>
> R.E.D. Server allows:
> (A) Ante_R.E.D. 2.0
> PDB files(s) ---> P2N file(s)
> (i) geometry optimization
> (ii) MEP computation
> (B) R.E.D. IV: four steps (iii) charge fitting
> (iv) ff lib. building
> P2N files(s) ---> mol2 file(s)
>
> ---
>
> A frcmod file contains missing force field parameters. If needed, it
> can be generated independently of the FF libraries by hand by looking
> at errors generated by LEaP or by using Antechamber.
>
> > To have closed shells I added extra hydrogens to the Ser where it would
> be
> > joined with the other amino acids.
>
> You can add hydrogen in your PDB file by using R.E.D. Server as well.
> See http://q4md-forcefieldtools.org/REDS/faq.php#19
>
> regards, Francois
>
>
>
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Received on Thu Jun 30 2011 - 16:30:03 PDT
