Hi,
> You are right.
> I found the difference between two crd files,
> but I still don't know why leap assigns coordinates in this way.
> I generated two crd files from two pdb files which are different from
> each other only in disappearing atom.
> However, when leap generates crd files from those pdb files, it
> exchanges the coordinates for HB2 and HB3 of cysteine residue.
> So HB2 atom of first crd file has the coordinate of HB3 atom of second
> crd file and vice versa.
>
> Do you know how I can fix this problem?
it looks like CYS and CYX have minimally different internal coordinates in
leap. This is a detail that would only matter when building systems for
TI. I spontaneously have no good idea instead of switching the coordinates
manually in your rst-files...
Thomas
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Mon Jul 23 2012 - 06:30:02 PDT
