AMBER Archive (2009)

Subject: Re: [AMBER] Parameters for HYP and CGU

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Thu Dec 17 2009 - 02:46:55 CST

Dear Rilei Yu,

> I have a peptide that contains HYP and CGU residues. And I cannot
> use leap to save them. Do any one know is there any force field in
> amber that can do this? Now, I used ff03 and gaff, but i failed do
> that.

You could use the R.E.D. tools to generate required fragments
(central, N-terminal and/or C-terminal) for your unusual amino-acid(s).

See http://q4md-forcefieldtools.org/

See the tutorial about R.E.D.-III.3
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#10
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#13
See the tutorial about R.E.D. Server/R.E.D.-IV
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#15
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#16
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#17
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24

& an example in R.E.DD.B. (among many others)
http://q4md-forcefieldtools.org/REDDB/projects/F-81/
about beta-carboxylato-L-aspartate from A. Ziemys

regards, Francois

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber