Well, impressive explanation! Thank you very much!<br><br>Steven<br><br><div class="gmail_quote">On Fri, May 11, 2012 at 4:38 PM, Richard Broadbent <span dir="ltr"><<a href="mailto:richard.broadbent09@imperial.ac.uk" target="_blank">richard.broadbent09@imperial.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">here is a simple example (for more complex ones see the existing<br>
residues in an aminoacids.rtp)<br>
<br>
assume molecule looks like<br>
<br>
A-B-C<br>
<br>
where the -'s are bonds<br>
<br>
with residues AAA, BBB, CCC containing the corresponding atoms,<br>
then the .rtp should contain something like:<br>
<br>
[ AAA ]<br>
[ atoms ]<br>
A typeA chargeA 1<br>
[ bonds ]<br>
A +B<br>
<br>
[ BBB ]<br>
[ atoms ]<br>
B typeB chargeB 1<br>
[ bonds ]<br>
B -A<br>
B +C<br>
<br>
[ CCC ]<br>
[ atoms ]<br>
C typeC chargeC 1<br>
[ bonds ]<br>
C -B<br>
<br>
the + and - define which direction the connection should go<br>
<br>
I hope that's helpful<br>
<br>
Richard<br>
<div class="HOEnZb"><div class="h5"><br>
On Fri, 2012-05-11 at 15:43 +0100, Steven Neumann wrote:<br>
> Dear Gromacs Users,<br>
><br>
> I created my own residues in aminoacids.rtp which each is formed of<br>
> one atom. I would like to somehow create bonds between then using<br>
> standart harmonic potential. Could you please advise how to do this?<br>
><br>
> Stevem<br>
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