[gmx-users] strange new H-H bond formation during MD

[Tsjerk Wassenaar]

Note that it should be CONECT and not CONNECT...

Tsjerk

On 10/24/06, Erik Marklund <erikm at xray.bmc.uu.se> wrote:
> 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
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> --
> 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
> erikm at xray.bmc.uu.se
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336