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On 10/11/2011 10:43 PM, James Starlight wrote:
<blockquote
cite="mid:CAALQopxRoMibXsrHx6YEQjra0bD6hF89DZ10o7x5bW=5e=G6DA@mail.gmail.com"
type="cite">Mark,<br>
<br>
The problem is that my .itp done for old gromos ff consist of
parameters for molecule wich has some specific groups wich not
preset in the gromos96 ff so pdb2gmx is not good decision :)<br>
</blockquote>
<br>
Then you'll have to work out how the old .itp worked, and how that
functionality works in the current force field and file format.
Chapters 4 and 5 are your friends here.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAALQopxRoMibXsrHx6YEQjra0bD6hF89DZ10o7x5bW=5e=G6DA@mail.gmail.com"
type="cite"><br>
By the way I'm intresting what changes were done in the dihedrail
terms since gromos87 ff.<br>
E.g I found topology wich consist of parameters for D-amino asids
and I want to compare it with L-analogs in gromos96 to find
possibe way to make such parametrisation in the gromos96<br>
<br>
<br>
James<br>
<br>
<div class="gmail_quote">
2011/11/10 Mark Abraham <span dir="ltr"><<a
moz-do-not-send="true" href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span><br>
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<div class="h5">On 10/11/2011 9:30 PM, James Starlight
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
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Dear Gromacs Users!<br>
<br>
<br>
I need tto convert topology.itp fule made for my
molecule for the old gromos87 force field to the form
wich would be suitable for the simulation with the
gromos96 force field.<br>
<br>
What main corrections should I do in my existing .itp
topology?<br>
</blockquote>
<br>
</div>
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Use pdb2gmx with gromos96 to find out the form of the
solution. Then adapt as necessary.<br>
<br>
Mark<br>
<font color="#888888">
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