[gmx-users] Large branched and crosslinked polymer

[Mark Abraham]

Luke Pestl wrote:
> Hi,
> I am new to gromacs and I am trying to model a system that has a protein 
> and a fairly large and complex random polymer.  I am having trouble 
> adding the polymer to the system.  PRODRG was useful with a small 
> segment of the polymer, but I would like to use a much larger molecule.  
> I thought I could enter the monomers into the rtp file, but because it 
> is randomly branched and cross linked I do not know if this is 
> possible.  The description of x2top sounded hopefull, and I thought that 
> it might be able to generate an rtp entry for me, but I cannot get the 
> program to work because I cannot find the n2t library files that it 
> requires (am I supposed to make these files, or should they have been in 
> the package somewhere?).
> Any suggestions as to how I should proceed would be greatly appreciated.

The intrinsic irregularity of your structure will require you to build 
structure by hand - or at least to write your own scripts to build them. 
You should build them out of structural monomers whose topologies are 
defined in an .rtp file and get pdb2gmx to generate the topology for 
each such molecule, in the same way that it works for amino acid 
polymers. Depending on your polymer, you will probably need to build 
your monomer topologies by hand in the .rtp file, by analogy.

Mark