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 -- Maria G. Technical University of Denmark Copenhagen
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