Hi Yongzhi,
It is also a good idea to look at RMSD profile for each domain separately
(superimpose only one domain of your protein on the same domain of the
crystal (starting) structire). If RMSD for a single domain is low, it's OK
and probably the high RMSD you observe for the whole protein arises from
changes in spatial arrangement of domains. But if you have high RMSD for
each domain as well, it might mean that your protein is unfolding.
best
marcin
Dr Marcin Krol
Zaklad Bioinformatyki Collegium Medicum UJ
Kopernika 7E
31-501 Krakow
tel/fax (012) 422-77-64
e-mail mykrol.cyf-kr.edu.pl
On Wed, 4 Aug 2004, Yongzhi Chen wrote:
> Dear Amber users/developers,
>
> I want to make sure if RMSD of 9.7 (fit) in a 2 ns GB
> MD is necessarily a problem. The protein consists of 3
> domains, 1278 residues. The ID is 3BTA. In the input
> file, I assigned igb=5.
>
> Any suggestion will be appreciate.
>
> Best,
> Yongzhi
>
>
>
>
> __________________________________
> Do you Yahoo!?
> New and Improved Yahoo! Mail - Send 10MB messages!
> http://promotions.yahoo.com/new_mail
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Thu Aug 05 2004 - 09:53:00 PDT
