Hi prof. David Case,
Thanks for your help, now my restraint problem has been solved.
Best wishes,
Rilei Yu
--- 10年4月2日，周五, case <case.biomaps.rutgers.edu> 写道：
发件人: case <case.biomaps.rutgers.edu>
主题: Re: [AMBER] How to perform backbone and residues restraint at the same time
收件人: "AMBER Mailing List" <amber.ambermd.org>
日期: 2010年4月2日,周五,下午9:57
On Fri, Apr 02, 2010, Rilei Yu wrote:
>
> Thanks for your help all the time. Now I came across a new problem: I
> want to restraint all the backbone of the protein, while the side
> chain of the residues in the binding site can be flexible. I just want
> to refine the binding modes of my ligand using less time and other
> purpose. Can anyone give me some suggestions?
>
> I have try many times, but it still does not work well. I find it cannot
> work for my two purposes together.
> ###
> ntr=1, restraintmask=':1-420.CA',
> /
> Hold the DNA fixed
> 500.0
> RES 1 92
> RES 94-183
You can use either restraintmask OR the group input, not both together.
Note also that 500.00 is way too large a restraint; consider values about 100
times smaller.
...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Apr 03 2010 - 03:00:02 PDT
