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
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