On Tue, 2006-10-24 at 04:59 +1000, Mark Abraham wrote: > Qiao Baofu wrote: > > Thanks. Now I understand what happens. > > > > But in the user-manual of VMD, it is said that only four Gromacs file > > (GRO, G96, XTC, TRR) and .pdb can be read by VMD. But only the .pdb > > contain the information of bond-connectivity (if I understand > > correctly). The point is that the output .pdb file from mdrun contains > > only the coordinate information! How can I tell VMD the > > bond-connectivity information?!! > > PDB files do not contain bond connectivity. By the look of > http://www.ks.uiuc.edu/Research/vmd/current/ug/node21.html, you can't > tell VMD your gromacs connectivity, unless you write your own plug-in to > VMD (hint, hint). You could also try asking the VMD mailing list. Your > simplest plan is likely to be to generate a PSF or PARM file with an > equivalent topology, for they are used in other MD codes to contain the > connectivity.
That's not entirely true. Normally, pdb files do not contain topological information, but they CAN do so through a CONNECT block. This is probably why VMD claims that ".pdb contain the information of bond- connectivity" (don't use vmd myself, just cited Bafou above). However, to my knowledge, gromacs completely ignores CONNECT blocks in pdb output/input, which is why you see atoms only, and no connection. /Erik > > VMD is showing these bonds because the H atoms are getting close enough > to qualify as bonded by its rules. As I suggested in my first reply, are > you sure that this proximity doesn't mean your simulation is broken > somehow? If so, that would also solve your problem - just not so usefully! > > > I used the "mol new myfile.gro autobonds 0" to see my molecules. > > Unfortunately, only atoms are displayed, no connection. > > Well, that's what that command asks it to do :-) > > Mark > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > 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 -- Erik Marklund, PhD Student, Molecular Biopcysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 4537 fax: +46 18 511 755 [EMAIL PROTECTED] _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users 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
