[gmx-users] Dealing with non-aminoacid residues

Mark Abraham Mark.Abraham at anu.edu.au
Tue Oct 6 23:09:47 CEST 2009

Englebienne, P. wrote:
> 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? 

No, that might be the right approach if you had lots of molecules to 
re-use, i.e. no bonds between them.

> Or generate .rtp, .hdb, .tdb and .atp files 
> for all the possible monomers I will be using? 

An .rtp will be necessary to use pdb2gmx to create topologies from 
structures. Your need for useful .hdb and .tdb will depend on your 
workflow. You should be able to recycle the .atp from whatever force 
field you're using.

Perhaps you should get some experience doing some tutorial material to 
get a handle on how these parts work together. Learn to walk before 
trying to design a machine to walk...

 > In the case of the
> latter, how can I direct GROMACS to read a local copy of the databases 
> instead of a global one?

GROMACS will search the working directory before the one in GMXLIB 
environment variable.


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