AMBER Archive (2005)

Subject: RE: AMBER: new residue

From: Douali, Latifa (latifa.douali_at_pnl.gov)
Date: Wed Jul 27 2005 - 15:45:17 CDT

Thank you for your suggestions

Here what I did Dr. Case
I created new residue called RES.
When I use the command "edit RES" in xleap, my monomer structure looks
fine.
I create a pdb file (using other software) for a polymer containing my
monomer with the residue name (RES). When I do
"> unit = loadpdb polymer.pdb"
>edit model"
The structure of my residue does not look planar as I expect. Using VMD
to edit my polymer.pdb file, the structure looks fine. Do I do something
wrong? My question is how can I make nucgen recognize my new residue?
Since I have this mismatch between Xleap and other software.
Or if you have any suggestion, I will gatfully appreciate it.

Many thanks

latifa

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 polymer".

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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