Dr Walker,
In that case I wont use all the parameters. I do not have CHARMM to prepare
those files.
However, I imagine that the atom charges are the same, regardless of using
CHARMM or Amber. Is this so?
Thanks,
David
On Wed, Jul 27, 2011 at 12:22 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi David,
>
> > Thanks Jason. I guess I'll have to manually go through the file and
> > find the
> > charges and parameters of the molecules I'm looking for.
>
> Be aware that the Charmm force field and the Amber force field are NOT
> directly compatible. You cannot simply copy parameters from one to the
> other. For example, Charmm typically uses Urey Bradley and CMAP terms which
> are not in the standard AMBER equation. Additionally the combining rules
> for
> the VDW are different and 1-4 nonbond interactions are scaled differently.
> Thus one cannot simply mix AMBER and CHARMM force fields within the same
> simulation. You can certainly do it but the results will be difficult to
> defend the validity of.
>
> In your case I suggest setting up your entire system using the charmm force
> field and writing a psf and crd file for the entire system. You can then
> convert this through chamber and run it in AMBER which will then run your
> simulation using the charmm force field as you defined in the psf.
>
> Good luck,
> Ross
>
>
> /\
> \/
> |\oss Walker
>
> ---------------------------------------------------------
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Adjunct Assistant Professor |
> | Dept. of Chemistry and Biochemistry |
> | University of California San Diego |
> | NVIDIA Fellow |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> ---------------------------------------------------------
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
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>
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>
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Received on Mon Aug 01 2011 - 10:00:04 PDT
