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 Wed May 25 2011 - 19:30:04 PDT
