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sounds like a good plan, but would this also work for a somewhat more
complicated system?<br>
my system looks more or less like this: <br>
<br>
thread= napthalimide-(CH2)12-succinamide-CH2-C-(phenyl)2<br>
<br>
the macrocycle consists of a coupleof phenyl rings bonded together via
amide groups.<br>
<br>
I think most of the atoms are in ffgmx.n2t so I'll give it a go.<br>
<br>
Peter<br>
<br>
David van der Spoel wrote:<br>
<blockquote cite="mid1096632660.26920.13.camel@vangogh.bmc.uu.se"
type="cite">
<pre wrap="">On Fri, 2004-10-01 at 14:00, Peter Zoon wrote:
</pre>
<blockquote type="cite">
<pre wrap="">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?
</pre>
</blockquote>
<pre wrap=""><!---->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.).
</pre>
<blockquote type="cite">
<pre wrap="">Peter
David van der Spoel wrote:
</pre>
<blockquote type="cite">
<pre wrap="">On Fri, 2004-10-01 at 12:07, Peter Zoon wrote:
</pre>
<blockquote type="cite">
<pre wrap="">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.
</pre>
</blockquote>
<pre wrap="">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)
</pre>
</blockquote>
<pre wrap="">
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</pre>
</blockquote>
</blockquote>
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