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

Qiao Baofu qiaobf at gmail.com
Tue Oct 24 10:06:35 CEST 2006

Yes. Gromacs can only generate the .pdb file without CONNECTION. I think it
is not only Gromacs but Material Studio that do like that. For more than 2
molecules, the softwares give only the coordinate data.

I find a top2psf.tcl file on the website of VMD (Script Library). It is said
this script can transfer .top file to .psf file, which can be recognized by
VMD.  But I don't know how to use it and the website of VMD doesn't give the
instrution how to use it.  :(

2006/10/24, Erik Marklund <erikm at xray.bmc.uu.se>:
> >
> > 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.

Sincerely yours,
Baofu Qiao, PhD
Frankfurt Institute for Advanced Studies
Max-von-Laue-Str. 1
60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529
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