AMBER Archive (2005)

Subject: AMBER: false bond created upon coordinate retrieval

From: Stern, Julie (jvstern_at_bnl.gov)
Date: Thu Apr 28 2005 - 16:29:38 CDT

Hello,
    I created my own molecule and system and used periodic boundary
conditions.
I postprocessed with ptraj with image to clean up the display of
periodicity.
I then saved a set of coordinates for a given frame from vmd as a pdb file,
loaded the pdb file back into leap of purposes of measuring geometry. But
leap is
saying there are a 20 or a 40 angstrom bond between two atoms and there are
parameters
that need to be defined for it those two atoms. However, there is no such
bond or connection between the two atoms, not in the original building of
the molecule. I also tried the un-postprocessed version without going
through
ptraj and got the same thing.

    How do I undo the affect of periodicity upon saving individual frames?

--Julie
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