Re: [AMBER] question about dihedral angles

From: David A Case <>
Date: Wed, 2 Dec 2020 08:51:08 -0500

On Wed, Dec 02, 2020, Karl Kirschner wrote:
>impose mymolecule {7} { {C1 C2 C3 C4 120.0} }

One point is this: the command above doesn't specific which atoms are to
be *moved* in order to make the dihderal be 120 degrees. Should the
program move C4 (and atoms bonded to it), or move C1 (and atoms bonded
to it)? Or do something else? This may not be important in some
workflows, but can be key in others.

The pyMol example has the same problem. Of course, its
documentation may be better in explaining what choices are made.

These sorts of manipulations are a natural for NAB (aka "molecular
awk"), but it has its own learning curve and documentation deficiencies.


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Received on Wed Dec 02 2020 - 06:00:04 PST
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