[gmx-users] tpr without top-file

David van der Spoel spoel at xray.bmc.uu.se
Fri Oct 1 14:11:00 CEST 2004

On Fri, 2004-10-01 at 14:00, Peter Zoon wrote:
> The problem with prodrg is that it removes all my hydrogen atoms and
> that it will not accept mocules of more than 2 parts. A rotaxane is a
> molecule which consists of a linear part, mostly saturated hydorcarbon
> (the thread) and a ring which goes around the thread. This ring (aka
> macorcycle) is held in place at one position by hydrogen bonds the tow
> ends of the thread are then blocked by bulky groups  and the ring is
> mechanically locked onto the thread. (see Brouwer et al SCIENCE 291
> (5511): 2124-2128 MAR 16 2001). By applying a photochemical stimulus
> the macrocycle moves from one position to another (since the hydrogen
> bond affinity is changed) and back again.
> So i need all the polar hydrogen atoms and prodrg deletes them.
> Writing a topology by hand is I think a rather time consuming job for
> a system of more then 250 atoms. This besides the fact that i would'nt
> really know how to write a topology from scratch.  Or could i take the
> topology from prodrg and easily add some hydrogen atoms?
If your molecule is just hydrocarbons with some alcohol groups you could
also try x2top. Copy the file $gmx/share/top/ffgmx.n2t to your working
directory, run x2top and adapt the ffgmx.n2t file until you get a
working topology (don't use it for further simulations unless you really
know what you're doing in terms of force field parameters etc.).

> Peter
> David van der Spoel wrote:
> > On Fri, 2004-10-01 at 12:07, Peter Zoon wrote:
> >   
> > > Hi all,
> > > 
> > > Here's the story. We wrote a program which converts trajectories from 
> > > Macromodel to xtc. We obtain a initial gro file and the trajectory in 
> > > xtc format. We would like to use the gromacs analysis routines to 
> > > analyze the trajectory. We a looking at a rotaxane in particular we want 
> > > to study the hydrogen bonds between the macrocycle and the thread and 
> > > the dihedrals within the thread.
> > >     
> > the problem I presume it the topology. How about generating one using
> > prodrg? Many analysis tools can substitute the tpr file for a gro/pdb
> > file but g_hbond needs the atom names and the connectivity.
> > g_dih actually also needs the topology, although some things can be done
> > with just an index file (g_angle, which also analyses dihedrals)
> >   
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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