[gmx-users] defining new residues?

Rahul B Kasat rkasat at ecn.purdue.edu
Thu Sep 28 20:50:41 CEST 2006

Hi Scott

You can use PRODRG (available online) for generating topologies. Then you 
dont have to worry about playing with pdb2gmx.


- Rahul

On Thu, 28 Sep 2006 scott.t.milner at exxonmobil.com wrote:

> Hello -- I am interested in using gromacs to simulate polymers.  Apparently
> the .rtp files within gromacs are defined for protein residues, not typical
> monomers being used in polymers.  I don't know anything about proteins, but
> I would think that there is a strong analogy between proteins and polymers,
> in that linear polymers are composed of a succession of monomers (often,
> just the same monomer repeated), joined by single covalent bonds.  Typical
> monomers I would be interested in are methylene (-CH2-), propylene
> (-CH(CH3)CH2-), styrene (-CH(C6H5)CH2-), and so forth.  It would be very
> convenient if I could add these structures as new "residues" to the
> definitions of some of the force fields (e.g., OPLSAA and GMX), so that I
> could use pdb2gmx to generate topology files for a simulation, without
> having to generate the topology files by hand.  Is there some documentation
> that describes the structure of the various files associated with a force
> field, and what information would then be required for defining new
> residues?
> Thanks for any help you can provide --
> Scott Milner
> ExxonMobil Research and Engineering
> 1545 Route 22 East
> Annandale, NJ  08801
> (908) 730-2309 phone
> (262) 313-2583 fax
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