[gmx-users] .itp file for polymer (Polystyrene)
merohisg at yahoo.co.in
Wed Mar 26 06:01:25 CET 2008
Thanks Mark for guiding me.
Mark Abraham <Mark.Abraham at anu.edu.au> wrote: Rohit wrote:
> I am trying to generate a polymer layer with 30 chains of 20 monomeric
> units using gromacs' genbox command. For that, I need to have .itp file
> for the single polymer chain (polystyrene). I have .itp file for styrene
> molecule, how can I make a .itp file for polymer chain using .itp file
> of styrene? I guess there must be some way to use parameters of styrene
> molecule to build up a .itp file for the polymer.
> I would appreciate If someone can help me with this.
For a given n, you can build an n-styrene .top file with pdb2gmx. For
this to work, you need a styrene .rtp file entry that defines head and
tail atoms in a manner analogous to the peptide .rtp file entries, and
probably you will also need to make .tdb entries to cap the chains. Read
the relevant sections of chapter 5 and the wiki thoroughly, and
experiment with this mechanism on peptides (where it already works)
before trying to build the elements for your system.
Once you have the .rtp and .tdb entries constructed, you give pdb2gmx a
structure file containing the 20-styrene molecule, and it uses the
residue numbering in that to infer the topology based on the .rtp entry.
Then you edit the .top file by hand to become a 20-styrene .itp file.
Then you can construct your 30-chain coordinate file somehow, #include
the 20-styrene .itp file, construct a .top file by hand, and make sure
its [ molecules ] entry has 30 styrene molecules. pdb2gmx might also be
able to handle the 30 20-styrene coordinate file directly with the right
command-line option, but I've never done it, so you're on your own there.
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