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
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