[gmx-users] How to specify conection between 2 molecule in the top file?
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
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
O \____ _____/ O
\ /Ca Cb\ /
\ / \
C1-----------C2 ??? C2-----------C1
/ \ /
/ \Ca__ ___Cb/ \
O / \
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