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Anton,<br><br>
Thank you for the replies.<br><br>
Yes, I know about and have been using the PRODRG server
program.<br><br>
<blockquote type=cite class=cite cite>So, what then is your problem? Do
you get [bonds], [angles] etc<br>
sections in your .top file? If so, are the parameters
missing?</blockquote><br>
Yes, it specifies between which ones the bonds, angles etc are.<br><br>
<blockquote type=cite class=cite cite>If you don't specify parameters in
your .rtp (it appears you<br>
don't), then you don't get parameters in your .top explicitly.<br>
In that case, parameters are taken from the [*_types] defenitions<br>
in your ff*.itp files. Much of this is also described in the<br>
manual...</blockquote><br>
Ahhh, OK. Sorry I was under the impression that it inserted all of
those values into the .top file. So the software calls up the
ff*bon.itp file as required for how the angels, bond constants etc should
be?<br><br>
<blockquote type=cite class=cite cite>Atom names are simply labels; you
can chose whatever you want.<br>
But the way you do it seems sensible. If you want
automatic</blockquote><br>
That is good to know. I just noticed that in the .rtp files
supplied that some use on convention of letters and others
numbers.<br><br>
<blockquote type=cite class=cite cite>hydrogen addition (requires .hdb
entries), you must name/number<br>
hydrogens systematically (described in the manual under 'Hydrogen<br>
database').</blockquote><br>
I picked that up from the manual and will be looking at that as I add
further residues etc.<br><br>
Thank you for your assistance. It is much appreciated.<br><br>
Catch ya,<br>
<x-sigsep><p></x-sigsep>
<b>Dr. Dallas Warren<br>
</b><i>Research Fellow<br>
</i>Department of Pharmaceutical Biology and Pharmacology<br>
Victorian College of Pharmacy<br>
Monash University<br>
<font color="#0000FF"><u>dallas.warren@vcp.monash.edu.au<br>
</u></font>+61 3 9903 9076</html>