What about approaching RED with NWChem? In my experience NWChem affords
reliable RESP charges and, on other basis, in particular plane waves in the
latest versions, I never considered to install Gamess or buy Gaussian.
Thanks
francesco pietra
--- FyD <fyd.q4md-forcefieldtools.org> wrote:
> Quoting Wei Chen <cwbluesky.gmail.com>:
>
> > I need to prepare a .prep file for a non-standard amino acid residue. I
> > followed the procedure in the tutorial
> > http://amber.scripps.edu/antechamber/pro4.html. As a test, I generated a
> > ACE-VAL-NME tripeptide. Going through all steps with antechamber and
> > gaussian 03, I get a prep file for Valine. However, the charge of each atom
> > is quite different from that in all_amino03.in. Could anybody tell me what
> > the reason is?
>
> You could also look at the tutorials .
> http://q4md-forcefieldtools.org/Tutorial/
>
> First of all, charge values in the AMBER force fields are not reproducible:
> See http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#3
> & in particular the section:
> "General information about molecular orientation and charge values"
>
> For information about the Duan et al. FF see:
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#7
>
> To compute charge values for central & terminal fragments see:
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#10
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#11
>
> regards, Francois
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
____________________________________________________________________________________
Be a better friend, newshound, and
know-it-all with Yahoo! Mobile. Try it now.
http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Jan 02 2008 - 06:07:12 PST
