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 Daniel -- 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. _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php