VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue Aug 22 2006 - 21:51:42 CDT

hi,

your .gro file is missing the simulation box dimensions
in the last line (at least three floating point numbers).
see the message in your vmd console window.
the unsuccessful read can also be detected from the
fact, that you have 22 atoms loaded, but 0 frames.
just add, e.g. 0.5 0.5 0.5 to your file and it loads well.

cheers,
 axel.

On 8/22/06, Marc Charendoff <mcharend_at_sbcglobal.net> wrote:
> Hello,
>
> I'm in the middle of trying to visually verify
> molecules that have been sent through the PRODRG
> server to generate .gro files for MD simulation. When
> I try to visualize, however, I get nothing. I'm afraid
> my coordinates are getting skewed in the process and
> could really use VMD's( and your) help. Any guidance
> you could provide would be appreciated.
>
> Regards, Marc
>
> Here's the file (it's short):
>
> PRODRG COORDS
> 22
> 1AHL CAS 1 -0.052 -0.933 -0.149
> 1AHL CAR 2 -0.108 -0.803 -0.090
> 1AHL CAQ 3 -0.010 -0.687 -0.117
> 1AHL CAP 4 -0.067 -0.557 -0.058
> 1AHL CAO 5 0.031 -0.441 -0.085
> 1AHL CAN 6 -0.025 -0.311 -0.026
> 1AHL CAM 7 0.073 -0.195 -0.053
> 1AHL CAL 8 0.016 -0.065 0.007
> 1AHL CAK 9 0.114 0.051 -0.021
> 1AHL CAJ 10 0.058 0.181 0.039
> 1AHL OAT 11 -0.067 0.198 0.047
> 1AHL CAI 12 0.153 0.291 0.089
> 1AHL CAH 13 0.087 0.428 0.072
> 1AHL OAU 14 0.004 0.447 -0.021
> 1AHL N 15 0.120 0.538 0.164
> 1AHL HAA 16 0.147 0.527 0.260
> 1AHL CA 17 0.107 0.667 0.095
> 1AHL CB 18 -0.033 0.697 0.048
> 1AHL CAA 19 -0.016 0.846 0.018
> 1AHL OAC 20 0.039 0.897 0.143
> 1AHL C 21 0.131 0.790 0.181
> 1AHL O 22 0.218 0.798 0.272
>
> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
  Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.