AMBER Archive (2005)

Subject: Re: AMBER: false bond created upon coordinate retrieval

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> 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 ... However, there is no such
> bond or connection between the two atoms ...

Does your pdb file contain TER cards (lines) after each molecule?
If not, leap may assume a bond exists between one molecule and the
next.

Bill
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