AMBER Archive (2006)

Subject: Re: AMBER: parameters for Nickel and iron

From: Rachel (comeonsos_at_googlemail.com)
Date: Tue Sep 19 2006 - 11:00:45 CDT

Hi, Fenghui,

Thanks for your reply, I have tried Antechamber, however, as far as i know,
Antechamber is only suitable for small molecules, is it? And the protein I
want to study is pretty big with several thousands atoms excluding hydrogen.

I really appreciate it if anyone could tell me where can I find such
parameters.

Best regards,
Rachel

On 9/19/06, Fenghui Fan <fenghui_fan_at_yahoo.com> wrote:
>
> I just want to discuss with you. Can you use
> Antechamber for this purpose? It is rather easy.
>
> I am looking forward to getting your reply on these
> especially to me.
>
> Best regards.
>
> Fenghui Fan
>
> --- Rachel <comeonsos_at_googlemail.com> wrote:
>
> > Dear all AMBER users,
> >
> > The protein I wish to study contains nickel atom
> > bonded with iron and CYS
> > residues (by S), while the iron atom is bonded with
> > CYS (by S) and HIS (by
> > ND). I am trying to create the frcmod file for these
> > non-standard metallic
> > ions and its bonded residues, can anyone tell me
> > where can i find the
> > parameters for Fe and Ni please? Thanks a lot in
> > advance!!
> >
> > With my best regards,
> > Rachel
> >
>
>
> __________________________________________________
> Do You Yahoo!?
> Tired of spam? Yahoo! Mail has the best spam protection around
> http://mail.yahoo.com
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>

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