Re: AMBER: new residue

From: David A. Case <>
Date: Wed, 27 Jul 2005 10:20:42 -0700

On Wed, Jul 27, 2005, Douali, Latifa wrote:
> The pdb file of the polymer looks fine when I load it in VMD.
> I expect my monomer structure (into the polymer) to be planar. In Xleap,
> the residue is palanar when I load it as a monomer but it is not the
> case within a polymer. I have to mention here that my polymer pdb file
> is created by another program. Is there a mismatch between the Xleap and
> the other softwares? Thanks

I think you need to be a lot more specific about what commands you are using.
It is not clear what you mean by "load it as a monomer", and "within a

The usual rule here is "tell us what you actually did (and what the result
was)". Telling us what task you were trying to accomplish is helpful, but
generally not enough.

Generally, you don't use LEaP to build three-dimensional models of structures,
although this is sometimes done. The more usual case is that you have (from
somewhere else) a pdb file with reasonable coordinates for the final molecule
you wish to examine.

....good luck...dac

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Received on Wed Jul 27 2005 - 18:53:00 PDT
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