[gmx-users] Dealing with non-aminoacid residues

[Andrea Muntean]

Hi Pablo,

I would write .rtp entries and so on for each monomer.

You copy the modified files into your working directory.

Have a great day,
Andrea

2009/10/6 Englebienne, P. <P.Englebienne at tue.nl>

>  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.
>
>
>
> Thanks!
>
> --
> 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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