[gmx-users] .itp file for polymer

[Mark Abraham]

David Huang wrote:
> hi
> 
> i'm new to gromacs and am trying to construct an initial configuration
> for a system of polymer chains. i've looked through previous posts to
> the mailing list (such as the one attached below) and read chapter 5
> of the gromacs manual and the wiki, but it is still not clear to me
> how to construct the .pdb file of the polymer chain to be used as
> input for pdb2gmx to produce the .top file of the chain.
> 
> all of the gromacs examples i've found for .pdb files of proteins have
> the polypeptides defined atomistically, rather than in terms of
> monomers (amino acids). but i presume that defining the monomer
> topology in the .rtp and .tdb files should allow the topology of the
> polymer to be defined in terms of monomer units or at least in terms
> of the coordinates of the backbone atoms. is this correct?

GROMACS is not set up to do general model-building tasks for you, beyond 
the limited functionality provided by the .tdb and .hdb files. 
Generating a structure from monomers is thus not a task it will do. 
Since you'll need a starting structure anyway, it is not such a great 
task to need one before you build your topology, if you want to use 
pdb2gmx. As I said last time, if you don't want to use pdb2gmx then you 
can build your .top file by hand and use whatever tools you like for 
building your initial structure.

Mark