[gmx-users] defining new residues?

[David van der Spoel]

Dongsheng Zhang wrote:
> It is possible to generate new "residues". First of all, you need to
> make a decision which force field you will use for your new residues.
> For example, you will choose opls. then you add one building block into
> ffoplsaa.rtp. As you read ffoplsaa.rtp, you can see that you need to
> specify atoms' name, type, and the partial charge, you also need to
> define bonds and the dihedral angle between atoms. When you build it,
> you need to refer ffoplsaanb.itp ffoplsaabon.itp and ffoplsaa.atp. You
> might modify aminoacids.dat, ffoplsaa-n.tdb' ffoplsaa-c.tdb as well.
> 
> 
> You can read the manual to get more information.
> 
> 
> On Thu, 2006-09-28 at 13:38 -0400, 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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an alternative that's in the works is the x2top program, which is 
simpler, since it is atom based, but you need just one configuration 
file. if you want to see a sample send me a coordinate file off-list. 
you will need at least the 3.3.1 CVS version for this though.

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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