[gmx-users] Generate topology file for Gromacs a from Accelrys or pdb file
Mark.Abraham at anu.edu.au
Tue Feb 12 23:54:27 CET 2008
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
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!
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