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Hi Rosa,<br>
<br>
You can read the paper on PRODRG to study how they parametrise.<br>
There's a topology builder for OPLS-AA:<br>
<a class="moz-txt-link-freetext" href="http://labmm.iq.ufrj.br/mktop/">http://labmm.iq.ufrj.br/mktop/</a><br>
<br>
There're also commercial tools (see some previous posts on the mailing
list) and you can also start with PRODRG and modify the files to have
the right parameters as in GMX.<br>
<br>
However, you should verify that your molecules are correctly
parametrised no matter what software you're using - run a simulation
with it and see if things look all right (e.g., if rings are not too
distorted, bonds are correct etc.) and try to get experimental
parameters to compare with.<br>
<br>
It has been stressed out a lot in the list that this is an advanced
issue - being familiar with MD and the FF you're using is a
pre-requisite to parametrisation. <br>
<br>
Good luck,<br>
Ran.<br>
<blockquote cite="mid20090525104146.A93B7BE407F@ws1-9.us4.outblaze.com"
type="cite">
<div><br>
Dear Ran<br>
<br>
Thanks for the reply. I think I `ve read some papers using PRODRG and
opls. However they didnt mention clearly that how they parametrized
their force field. Just do you know any alternative software. As I
checked many softwares but I couldnt find any to create .itp file at
the same time. Thank you.<br>
<br>
Regards<br>
Rosa<br>
</div>
<br>
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