[gmx-users] conversion of xtc to g87 (amber) format trajectory files/bounding box problem?

Daniel Rigden drigden at liverpool.ac.uk
Mon Apr 23 16:38:33 CEST 2007

Hi everyone

I'd like to convert my Gromacs trajectory to an Amber format for use
with the CAVER program.  Reading round, it seems that Amber is
equivalent to the g87 format so I can use trjconv to produce the file.
This all seems to work well (the file gets read in and processed) except
for a problem with the bounding box.  

When caver works on a PDB file and generates its own box it comes out
like this
Grid: [63 82 76]
  BBox: (39.198000 6.232000 19.088000 ,89.027000 71.759000 79.758000 )

The box that gets read from the g87 trajectory looks like this
Grid: [7 9 7]
  BBox: (3.307000 0.906000 1.856000 ,8.843000 7.670000 7.336000 )

>From other reading there seems to be a unit issue (A vs nm) in the
Gromacs/Amber comparison.  The two boxes above are quite close to
10-fold different in all dimensions.  Is this the source of my problem?
How can I work around this?

Thanks in advance for your help


Dr Daniel John Rigden                     Tel:(+44) 151 795 4467
School of Biological Sciences             FAX:(+44) 151 795 4406
Room 101, Biosciences Building
University of Liverpool
Crown St.,
Liverpool L69 7ZB, U.K.

More information about the gromacs.org_gmx-users mailing list