RE: AMBER: new residue

From: Ross Walker <>
Date: Wed, 27 Jul 2005 09:54:14 -0700

Dear Latifa,

> 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

Leap uses the unit only for topology information, and atom positions when
atoms are missing. If you are loading a pdb file the atom positions as
specified in the pdb file will be used and the coordinates of the individual
unit will be ignored.

> 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

You need to make sure that the residue name, atom names and atom ordering in
your pdb file match those in the monomer unit you created. If they do then
you shouldn't have a problem.

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel: +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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