Re: [AMBER] unique atom names

From: case <>
Date: Fri, 10 Aug 2012 20:54:37 -0400

On Fri, Aug 10, 2012, Chris Chris wrote:

> I performed some docking in vina- added all hydrogens back with YASARA
> and loaded the pdb into amber nut it shows a fatal error that not all
> atoms have a unique type. zCould someone point me to how to assign
> unique 'types' to atoms. Is there a program that does so?

Generally: it is *much* more helpful to report the exact (Amber) commands you
gave, and the exact error message. "...loaded the pdb into Amber" could mean
a lot of things, and seeing the actual error message is often very helpful.

It sounds like you have a molecule that is not a standard protein or nucleic
acid. In that case, you have to create a library file that assigns atom types
to each atom, and load this into tleap before you issue the loadPdb command.
See, for example, Tutorial B4.


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Received on Fri Aug 10 2012 - 18:00:02 PDT
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