[gmx-users] Dealing with non-aminoacid residues
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
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