Re: [AMBER] bond connections

From: David A Case <>
Date: Thu, 3 Dec 2015 08:26:15 -0500

On Thu, Dec 03, 2015, mohammad r wrote:
> As I am new to the amber, I want to know that when I’mgenerating
> my system, is it necessary to define all the bonds between atoms
> andmolecule?

Generally (if I understand the question), the answer is "no". Unless
you have cross-links (bonds between molecules, or that are not always
present), you don't need to define bonds.

> There issomething wrong with the internal bonded interactions.

There is not enough information here to help out. Use parmed to print which
bonds are in the prmtop file. We can help on the Amber side if there are too
few or too many bonds. It is less clear whether people on this list will be
experts in the conversion to gromacs. I'd certainly suggest running a
minimization or short dynamics in Amber before converting formats to GROMACS.


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Received on Thu Dec 03 2015 - 05:30:04 PST
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