[gmx-users] defining new residues?
David van der Spoel
spoel at xray.bmc.uu.se
Thu Sep 28 21:07:36 CEST 2006
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
>> 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
>> gmx-users mailing list gmx-users at gromacs.org
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> gmx-users mailing list gmx-users at gromacs.org
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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 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
More information about the gromacs.org_gmx-users