AMBER Archive (2009)

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

From: Rilei Yu (yulaomao1983_at_yahoo.com.cn)
Date: Wed Dec 16 2009 - 23:57:13 CST

Hi Dr. Jason Swails,

Based on you suggestion, I just did everything in the tutorial, meanwhile, I adopt some dihedral parameters from .frcmod in the amber package. Now, my problem has been solved! I know people use gossan03 to calculate the charges, but here I just use antechamber to do this job instead. I donot know my calculation can be accurate to my simulation or not.

Thanks for your suggestion!

Rilei Yu

--- 09年12月17日，周四, Jason Swails <jason.swails_at_gmail.com> 写道：

发件人: Jason Swails <jason.swails_at_gmail.com>
主题: Re: [AMBER] Parameters for HYP and CGU
收件人: "AMBER Mailing List" <amber_at_ambermd.org>
日期: 2009年12月17日,周四,上午11:58

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

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