AMBER Archive (2007)

Subject: Re: AMBER:

From: Vladimir Tchoupakhine (chupvl_at_gmail.com)
Date: Wed Jan 10 2007 - 10:51:46 CST

You have to provide us with additional info
How big is your enzyme
And were did you did minimization? AMBER or other software - what parameters
you have used?

Vladimir

On 1/10/07, Steve Seibold <seibold_at_chemistry.msu.edu> wrote:
>
> Hello Amber
>
> I have a crystal structure of a large enzyme (resolution ~ 2.5Angstroms).
> When up load my structure (without hydrogens) in to xleap, xleap then adds
> hydrogens to my structure. However, it then tells me when I do a "check"
> unit that the hydgrogens it has added are "Warning: Close Contact" between
> atoms of the protein and the hydrogens it has added. There are 170 warnings
> of this kind. I have tried to energy minimize the structure, but it is
> proving to be very, very difficult with the repeat warning (in sander during
> minimization) "repeated limit failure" and stops the minimization. I have
> tried every routine (i.e. different strategies for minimization..i.e.
> different ncycle and maxcycle) and nothing is working. Can you some one give
> me some advice?
>
>
>
> Thanks, Steve
>
>
>
>
>

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