Jacob Harvey wrote:
Dear All,
I am trying to use the OPLS-AA force field to model some imidazole
containing compounds. I've noticed that imidazole units are referenced
in the ffoplsaa.atp file as the following:
opls_557 14.00670 ; N1 in imidazole
opls_558 12.01100 ; C2 in imidazole
opls_559 14.00670 ; N3 in imidazole
opls_560 12.01100 ; C4 in imidazole
opls_561 12.01100 ; C5 in imidazole
opls_562 1.00800 ; H1 in imidazole
opls_563 1.00800 ; H2 in imidazole
opls_564 1.00800 ; H4 in imidazole
opls_565 1.00800 ; H5 in imidazole
But there are no parameters for these atoms in the ffoplsaa.rtp file.
Does anyone know how I can go about naming these atoms in my pdb file?
Thank you in advance.
Not every compound is present in a .rtp file. Check out its contents and you'll
see what it has - pretty much just amino acids. The charges on each atom are
not specific to an atom type, they are specific to a chemical species for which
the parameterization scheme has been conducted. Lennard-Jones parameters are
specified in ffoplsaanb.itp.
I suggest a thorough read of Chapter 5 of the manual to understand the contents
of these database-type files, and how they are used in assembling a topology.
-Justin
Jacob Harvey
--
--
Jacob Harvey
Graduate Student
University of Massachusetts Amherst
[email protected] <mailto:[email protected]>
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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