in my opinion, ff99 for proteins should never be used. use ff99SB or ff03.
others may suggest what is best for DNA- I think ff94 or ff99 and I do not
think
there is any such thing as ff03 for DNA. others may know more.
On 2/13/07, Catein Catherine <askamber23.hotmail.com> wrote:
>
> Dear Amber Users,
>
> I am new to AMBER, I could like to do a stimulation for a complex with
> protein, DNA and organic coactivator. I read from the literature that
> para99 is better for DNA stimulation? GAFF is better for organic
> compounds.
> Is it true that they are the best? Is it also true for protein?
>
> Follow the tutorial 1, I used the command
> usr/local/amber8/dat/leap/cmd/leaprc.ff99. Read the xxx.lib and xxx.frcmod
> from Antechamber. Does it call for the best force field parameters for
> protein, DNA and organic compounds?
>
> If not, what should I do to make use of the best forces field for
> different
> components?
>
> Best regards,
>
> Catherine
>
> _________________________________________________________________
> Learn English via Shopping Game, FREE!
> http://www.linguaphonenet.com/BannerTrack.asp?EMSCode=MSN06-03ETFJ-0211E
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Feb 18 2007 - 06:07:05 PST
