[gmx-users] can gromacs read amber trajectory

Lydia aether2006 at gmail.com
Sat Feb 18 03:16:51 CET 2006

   I heard that previous version gomacs can read amber trajectory file by
changing name to .g87.  So I tried this command after renaming amber
trajectory to .87:

     g_gyrate -f nmwt.g87 -s nmwt.tpr -n index.ndx

     I got the following Segmentation fault error:
Selected 1: 'Protein'

 Select File Format
1. XYZ File
2. XYZ File with Box
3. Gromos-87 Ascii Trajectory
4. Gromos-87 Ascii Trajectory with Box

Choice: 4


Number of atoms ? 17351
Time between timeframes ? 1

Reading frame     790 time  791.000
Back Off! I just backed up gyrate.xvg to ./#gyrate.xvg.4#
Segmentation fault

     Have someone had successful experience of using amber trajectory in
gromacs 3.3? Also  in trajectory, I have 800ps which means 800 sets of
coordinates and boxsize but it seems always read 790 sets (based on the
number of read frames prined out on screen).  If I try some other amber
trajectory with 100 sets, it seems to read to 90 sets only. Is it right? Any
suggestion is welcome..
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