AMBER Archive (2006)

Subject: Re: AMBER: neutral N-terminal amino-acid parameters for ff03

From: FyD (fyd_at_u-picardie.fr)
Date: Sat Aug 05 2006 - 03:16:23 CDT

Quoting Vlad Cojocaru <Vlad.Cojocaru_at_eml-r.villa-bosch.de>:

> I am interested in using a neutralized N-terminal PRO (or GLY) in a
> protein simulation using ff03. I would like to ask whether somebody has
> already developed such parameters and is willing to share them.

I am a little late... After reading the emails of C. Simmerling, Y.
Duan & R. Luo, _if_ you wish to derive new terminal residues for the
ff03 FF, you have many examples in R.E.DD.B.
http://www.u-picardie.fr/labo/lbpd/REDDB/ you could use.

CENTRAL RESIDUES
Duan et al. FF//Central fragment of S-methyl-L-cysteine
http://www.u-picardie.fr/labo/lbpd/REDDB/up/F-70/
Cornel et al. FF//Central fragment of S-methyl-L-cysteine
http://www.u-picardie.fr/labo/lbpd/REDDB/up/F-69/

Duan et al. FF//Central fragment of S-sulfonate-L-cysteine
http://www.u-picardie.fr/labo/lbpd/REDDB/up/F-68/
Duan et al. FF//Central fragment of sulfonate-L-cysteine
http://www.u-picardie.fr/labo/lbpd/REDDB/up/F-66/

Cornel et al. FF//Central fragment of AIB residue
http://www.u-picardie.fr/labo/lbpd/REDDB/up/F-3/

TERMINAL RESIDUES
Cornel et al. FF//N-terminal charged fragment of AIB residue
http://www.u-picardie.fr/labo/lbpd/REDDB/up/F-7/
Cornel et al. FF//C-terminal charged fragment of AIB residue
http://www.u-picardie.fr/labo/lbpd/REDDB/up/F-11/
Cornel et al. FF//N-terminal neutral fragment of AIB residue
http://www.u-picardie.fr/labo/lbpd/REDDB/up/F-15/
Cornel et al. FF//C-terminal neutral fragment of AIB residue
http://www.u-picardie.fr/labo/lbpd/REDDB/up/F-19/

and even more... Please, use the _listproject_ tools.

regards, Francois

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu