VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Nov 26 2002 - 11:06:20 CST

Hi Vlad, VMD-L,
  I have found and fixed this bug. VMD 1.8 beta 6 will include an
updated AMBER parm file reader plugin. There was an error in a
piece of safety check code caused by 0-based and 1-based indexing
differences. The AMBER 7 reader was already correct, so this only
affects the reader for the older AMBER 4/5/6 files.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Nov 26, 2002 at 02:24:59PM +0100, Vlad Cojocaru wrote:
> Dear vmd users,
> There is a funny behaviour of all the vmd 1.8 versions when loading
> amber parameter and coordinate files.
> The VMD program is skipping the bond between the last two atoms so that
> for instance an H3' end hydrogen of an RNA strand remains "in the air"
> This does not happen with vmd 1.7.1.
> The parameter files are generated with amber6
> I know this is not something very very important but maybe somebody can
> take a look at it.
> Best wishes,
> vlad
>
> --
> Vlad Cojocaru
> Max Planck Institute for Biophysical Chemistry
> Department: 060
> Am Fassberg 11, 37077 Goettingen, Germany
> tel: ++49-551-201.1389
> e-mail: Vlad.Cojocaru_at_mpi-bpc.mpg.de
> home tel: ++49-551-9963204
>
> 

-- 
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