[gmx-users] Dealing with non-aminoacid residues

Englebienne, P. P.Englebienne at tue.nl
Tue Oct 6 13:10:54 CEST 2009

Hi all,

I'm looking to perform simulations on a series of synthetic co-polymers containing a variety of building blocks. I will be testing different sequences of the monomers, therefore I am looking for a way to streamline the generation of the topologies.

I have been reading Chapter 5 of the manual, but I'm still a bit puzzled about how to proceed to build topologies for my system. Should I make an .itp file for each monomer? Or generate .rtp, .hdb, .tdb and .atp files for all the possible monomers I will be using? In the case of the latter, how can I direct GROMACS to read a local copy of the databases instead of a global one?

I'll appreciate any pointers in this direction.


Pablo Englebienne, PhD
Institute of Complex Molecular Systems (ICMS)
Eindhoven Univeristy of Technology, TU/e
PO Box 513, HG -1.26
5600 MB Eindhoven, The Netherlands
Tel +31 40 247 5349

"Progress is made by lazy men looking for easier ways to do things." - Robert A. Heinlein

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