Dear Mark,<br><br>I can most certainly express myself in an exteremely dry and stuffed up manner if it is more to your liking. It seems that my previous 20 postings weren't critized at all ,even though my posts were utterly incomprohensible and my english apolling. But<br>
I promiss to do my absolut best and from now on my post will contain only the utmost<br>reverance.<br><br>Would you be kind to clearify the second part of may question? Namely, could "+" and "-" signs, mentioned in the manual and used in the rtp files be helpfull to me<br>
in this case? <br><br>Yours Gratefully,<br>Frankie Montenegro<br><br> <br><br><br><div class="gmail_quote">On Sun, Apr 6, 2008 at 6:20 AM, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>> wrote:<br>
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<div>Frankie Montenegro wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
Hi everyone, I have a question regarding a forcefield build.<br>
Is there a way to specify in the topology file how to bond two molecules<br>
one to another?<br>
</blockquote>
<br></div>
The GROMACS implementation of bonded interactions doesn't permit them between atoms in different [ molecules ] sections. What you put in such a section, however, is your own business.<div><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
So this thing, a halfaring + carboxyl on the left is one molecule and similar<br>
thing on the right is the other molecule. <br>
</blockquote>
<br></div>
No, they are fragments of molecules.<div><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
But I need to bond carbons a and b<br>
to get the full ring. Is this possible? Please don't ask me why I didn't make the<br>
whole thing one molecule (it is convinient for some other reason) I am using my<br>
own bonds angles and dihedrals, not "virtual sites" or any of that stuff.<br>
Is that "+" and "-" stuff from rtp file going to work here? Thanks, Frankie<br>
</blockquote>
<br></div>
A measured approach and a respectful tone is always a good idea when asking for free advice. If your knowledge of the topology file syntax was so good that your assumption (that you don't need to defend part of your unusual choice) was actually valid, then you'd know enough to solve the problem that it was creating :-)<br>
<br>
Mark<br>
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