[gmx-users] Generate topology file for Gromacs a from Accelrys or pdb file

[Mark Abraham]

Tandia, Adama wrote:
> Dear ALL,
> 
> I have generated from Accelrys (Materials Studio) a structure composed
> of a substrate topped by a layer of organic molecules. The structure can
> be saved into a .pdb format.
> 
> Is there out there a tool that I could use to generate the corresponding
> topology file for Gromacs?

The best advice on this topic is probably in here 
http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation

Arbitrary organic molecules will require you to generate a topology for 
each type of molecule. This is do-able, but not trivial.

Roughly speaking, pdb2gmx is set up to handle peptides and nucleic acids 
that have standardized atom and residue names. It is possible to extend 
this set to other species with the .rtp file. See chapter 5, and be 
prepared to work hard!

Mark