Hi,
md2.png seems to show a glutamine (left) and tyrosine (right) that are too
close to each other. PyMOL just draws bonds between them because they are
too close. I wouldn't say that the structure is a 'mess', just that the two
residues are much too close.
Are one or both residues fixed with ibelly?
Obviously, more details are needed for further explanations/help.
Marc
On 26 May 2011 03:21, Jason Swails <jason.swails.gmail.com> wrote:
> On Wed, May 25, 2011 at 9:40 PM, qiaoyan <qiaoyan.dicp.ac.cn> wrote:
>
> > Dear amber users:
> > I want to use ibelly to fix part of my protein, when I set ntb=1,ntp=0
> (
> > md1.in), there are four cavities in the obtained structures (md1.png).
>
>
> This is actually just 1 cavity. Caused by an unphysically large box
> generated by leap, as I'm sure you know (and alleviated with constant
> pressure MD).
>
>
> > when I set ntb=2,ntp=1 (md2.in), the obtained structure is a mess
> > (md2.png).
>
>
> This picture is too zoomed-in for me to tell what's going on or if anything
> is in fact messed up with that image. Perhaps others with more experienced
> eyes will laugh at my inability here, but the picture is not very
> descriptive to me.
>
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Thu May 26 2011 - 01:30:03 PDT
