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On 1/01/2012 7:45 AM, Lara Bunte wrote:
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cite="mid:1325364343.83117.YahooMailNeo@web29405.mail.ird.yahoo.com"
type="cite">
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<div>Hello</div>
<br>
I have two questions. <br>
<br>
First question:<br>
If you parameterize a force field (which means that you make
changes in atomtypes.atp, create a new .rtp and a .hdb file,
make changes in ffnonbonded.itp, create a residuetypes.dat file
and finally make symbolic links to gromacs) and you use pdb2gmx
to get a topology file (topol.top) and this file has not all
informations or something is wrong what is better: <br>
<br>
1.) Try to fix missing or false information in the topology file
(detective work in the topology)<br>
<br>
or should one<br>
<br>
2.) Try to fix something in the created and modified files of
the force field and parametrization<br>
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</blockquote>
<br>
If you have done a complete parameterization and constructed a
complete way for pdb2gmx to built a topology from a coordinate file
then the problem cannot arise. If you haven't done the former, then
go back and do it. If you haven't done the latter, then it is
probably right to fix the contents of the force field directory
(rather than the produced topology) on the theory that you may want
to use the force field again some time.<br>
<br>
<blockquote
cite="mid:1325364343.83117.YahooMailNeo@web29405.mail.ird.yahoo.com"
type="cite">
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255); font-family: times new roman,new york,times,serif;
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Second question:<br>
This question is implied in someway: If everything in the
parametrization is correct will be the topology you get by
pdb2gmx alway correct for further calculations? <br>
<br>
<br>
To summarize: If someone has bad (even false) topology, should
you try to fix the topology or is a bad topology always a strong
identification for bad parametrization?<br>
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</blockquote>
<br>
They're orthogonal. The topology expresses a particular combination
of the parameters that implements a model. Both topology and
parameters have to be right for the model to work, and failure
doesn't localize the problem to one or the other aspect. Just as
with writing, even if the parser (grompp) thinks the words you are
using make grammatical sense (no error, so sufficient parameter
values and connectivity), only you can judge whether the way in
which you have followed the rules should make for a meaningful
sentence (valid model).<br>
<br>
Mark<br>
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