Re: [AMBER] Reading chemical bonds from par7 files

From: David A Case <>
Date: Sat, 17 Jan 2015 09:55:48 -0500

On Fri, Jan 16, 2015, Francesco Pietra wrote:

> if ParmEd reports that a bond exists, then the prmtop defines
> that bond... VMD *should* report all bonds when loading a prmtop

Are the missing bonds in VMD between two different molecules (i.e. with
different chain ID's, or with a TER card between them)? Or, is there anything
that is different about the bonds that VMD shows and the ones that it misses?
Can you make a small example that illustrates the problem?


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Received on Sat Jan 17 2015 - 07:00:02 PST
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