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!
--- 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>
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
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
> AMBER mailing list
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
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