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On 7/02/2012 2:26 AM, Qinghua Liao wrote:
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<div class="gmail_quote">Dear GMX users,
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<div>We are trying to do a simulation of a protein attached to a
small molecules, how should I do to setup the system? For the
parameters of the small molecule, I got it from ATB sever,
however I don't know how to bond the small molecule and the N
terminal of protein.</div>
</div>
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<br>
The general solution is to use <a
href="http://www.gromacs.org/Documentation/File_Formats/specbond.dat">http://www.gromacs.org/Documentation/File_Formats/specbond.dat</a>
to allow pdb2gmx to learn about the bond to the new molecule. As you
will see in your [bonds] section, you have no bond to your new
residue.<br>
<br>
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<div class="gmail_quote">
<div>For gro file, it is ok, but for the topology file, I tried
to merge the parameters of small molecule and the topology
file together, and then renumber the atom number, and the
grompp worked. But when I wanted to do the geometry
optimization, it did not work. Here is the error:</div>
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<div>Fatal error:</div>
<div>There is no domain decomposition for 4 nodes that is
compatible with the given box and a minimum cell size of
3.52902 nm</div>
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<br>
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/Documentation/errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm">http://www.gromacs.org/Documentation/errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm</a><br>
<br>
You have set up your "small" molecule with only three charge groups.
mdrun functions as a large number of loops over interactions between
and within charge groups. The size of your large charge groups
creates a large lower bound on the number of atoms that have to be
present on each processor of a parallel simulation, and your number
of molecules is unsuitable for this. You need to investigate how to
generate charge groups that are both smaller and consistent with the
force field.<br>
<br>
Mark<br>
<br>
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<div>
I guess it is still a problem of the setup of the system,
the attachments are the gro and top files for the system. So
could someone give me some suggestions? Thanks very much!</div>
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-- <br>
Best Regards,
<div><br>
</div>
<div>Qinghua</div>
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