AMBER Archive (2006)

Subject: Re: AMBER: respin file

From: Fenghui Fan (fenghui_fan_at_yahoo.com)
Date: Sun Nov 26 2006 - 18:42:09 CST

Hi Ilyas Yildirim,

The thing is that the ZN is coupled by the CYM. And
the parameters for the ZN-SG of the CYM is missing.
Thus I need a kind of frcmod file.

Best regards.

Fenghui Fan

--- Ilyas Yildirim <yildirim_at_pas.rochester.edu> wrote:

> > Somebody treat the bond between the SG of CYM and
> the
> > ZN as a covalent bond. I have tried this way, the
> > situation is that the prepin file of the
> CYM-ZN.pdb
> > lackes the information of the ZN and the last two
> > atoms (I think the last 2 atoms should be ZN),
> thus in
> > the frcmod file, there is no information on the ZN
> > related bonds.
>
> ZN is not an organic molecule, so creating the
> necessary force field
> parameters is not that easy. If someone has already
> created those
> parameters for ZN, use those parameters.
>
> > The other question is about the command you
> mentioned:
> >
> >
> > antechamber -i CYM.pdb -fi pdb -o cym.in -fo gcrt
>
> This command will create a gaussian input file,
> which u will run using
> gaussian. After getting the gaussian output file, u
> can use antechamber
> -again- to get the resp charges.
>
> One other thing is that, there is already a CYM
> residue defined in the
> amber force field; so u dont need to do anything. As
> I wrote in my prev.
> email, I assumed that u are trying to get the resp
> charges for this
> particular molecule. As CYM residue is already
> defined in the force field,
> I dont think that u need to do any gaussian
> calculation and get the resp
> charges.
>
> Best,
>
> --
> Ilyas Yildirim
>
>
---------------------------------------------------------------
> - Department of Chemisty - -
> - University of Rochester - -
> - Hutchison Hall, # B10 - -
> - Rochester, NY 14627-0216 - Ph.:(585) 275 67
> 66 (Office) -
> - http://www.pas.rochester.edu/~yildirim/ -
>
>
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