AMBER Archive (2006)

Subject: Re: AMBER: manual/prmtop/missing bonds section

From: David A. Case (case_at_scripps.edu)
Date: Wed Jul 05 2006 - 11:09:06 CDT

On Mon, Jun 26, 2006, David Mobley wrote:
>
> Maybe this is just my confusion, but if this is correct, where does
> AMBER get the bond connectivity information from?

It gets it from the "unit" you have loaded (methane in your case). But it's
not clear from your description exactly what you are changing that causes the
bonds to disappear. Try changing just one H to dummy, etc. to try to narrow
down the symptoms.

....dac

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