VMD-L Mailing List
From: Demian Riccardi (riccardi_at_chem.wisc.edu)
Date: Thu May 29 2008 - 13:18:09 CDT
- Next message: Axel Kohlmeyer: "Re: Exceeded maximum number of bonds"
- Previous message: Paul Schlesinger: "vmd_init"
- Next in thread: Axel Kohlmeyer: "Re: Exceeded maximum number of bonds"
- Reply: Axel Kohlmeyer: "Re: Exceeded maximum number of bonds"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
Hello,
I'm trying to an visualize elastic network model of a protein where
the bonds are long and the number of bonds/per atom exceeds physical
norms. I generate a psf which has 758 bonds, but when I read it in
only 268 register with VMD. Does VMD purge excessive bonds or does it
just complain (as written below) and do what it's asked to do? If
it's the latter, then there's possible something wrong with my psf.
Demian
error message:
ERROR) MolAtom 24: Exceeded maximum number of bonds (12).
ERROR) BaseMolecule: Excessive bonding errors encountered, perhaps
atom coordinates are in the wrong units?
ERROR) BaseMolecule: Silencing bonding error messages.
- Next message: Axel Kohlmeyer: "Re: Exceeded maximum number of bonds"
- Previous message: Paul Schlesinger: "vmd_init"
- Next in thread: Axel Kohlmeyer: "Re: Exceeded maximum number of bonds"
- Reply: Axel Kohlmeyer: "Re: Exceeded maximum number of bonds"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]