VMD-L Mailing List

From: Marc Charendoff (mcharend_at_sbcglobal.net)
Date: Tue Aug 22 2006 - 21:03:41 CDT

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