[gmx-users] How to specify conection between 2 molecule in the top file?

Frankie Montenegro frankie.montenegro at gmail.com
Sun Apr 6 14:05:38 CEST 2008

Hi everyone, I have a question regarding a forcefield build.
Is there a way to specify in the topology file how to bond two molecules
 one to another?

So this thing, a halfaring + carboxyl on the left is one molecule and
 thing on the right is the other molecule. But I need to bond carbons a and
 to get the full ring. Is this possible? Please don't ask me why I didn't
make the
whole thing one molecule (it is convinient for some other reason) I am using
 own bonds angles and dihedrals, not "virtual sites" or any of that stuff.
Is that "+" and "-" stuff from rtp file going to work here? Thanks, Frankie
                       H                                 H
  O                     \____                  _____/                      O
     \                   /Ca                        Cb\                    /
      \                 /                                  \
       C1-----------C2            ???                 C2-----------C1
       /               \                                    /
      /                 \Ca__                  ___Cb/                   \
    O                  /                               \
                       H                                   H
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080406/638aa80b/attachment.html>

More information about the gromacs.org_gmx-users mailing list