[gmx-users] writing patches to combine two molecules into a dimer and getting the combined topology out

maria goranovic mariagoranovic at gmail.com
Fri Jun 4 10:50:14 CEST 2010

Dear Friends

I am looking to make the topology of a lipid bonded to a peptide. Although
this can be done by defining a new residue in the .rtp, this method may not
be the best if I want to repeat the procedure for different residues on the
peptide. Is it possible in gromacs to write a patch (like in CHARMM), where
one could combine two molecules using some sort of patch?  This is probably
implemented for proteins anyway, when amino acids are polymerized. The idea
is to have individual topologies and coordinates of the lipid and amino
acid, and writing some sort of patch to combine these two, by making new
bonds, and elminating some old ones. What would be the best (not necassarily
the easiest??) to do this?


Maria G.
Technical University of Denmark
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