AMBER Archive (2009)

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

From: Jason Swails (jason.swails_at_gmail.com)
Date: Wed Dec 16 2009 - 21:58:02 CST

Rilei,

When AmberTools 1.3 is released (I believe in a week or two), it will
have a file all_amino08.lib that has parameters for hydroxyproline.

However, for CGU, (gamma carboxy glutamate? that's what a google
search told me), there is no such file. However, you can follow the
sustiva tutorial ( www.ambermd.org/tutorials ) on creating your own
custom residues to teach you how to create an frcmod file from gaff
and/or the Amber force field.

This method can also be used for HYP, of course, if you're so
inclined. The tutorial and manual should help you get this figured
out.

Good luck!
Jason

2009/12/16 Rilei Yu <yulaomao1983_at_yahoo.com.cn>:
> Dear amber users,
>
> 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.
>
> Furthermore, can anyone give me some suggestions that I help me solve my problem?
> Thanks for your help!
> Rilei Yu
>
>
> ___________________________________________________________
> 好玩贺卡等你发，邮箱贺卡全新上线！
> http://card.mail.cn.yahoo.com/
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> 

-- 
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032

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