On Thu, Aug 08, 2013, egeh00 wrote:
>
> It seems that the sigma value in OPLS is much bigger than that in other
> FF. For example, the atomtype o in the glycam, gaff and opls are listed
> as below.
> Glycam_06h.dat "O 1.6612 0.2100 OPLS"
> gaff.dat "o 1.6612 0.2100 OPLS"
> OPLS_parm.dat "O 1.6 0.20"
> opls.info " O 2.96 0.21 "
First, please realize that the "opls" file in $AMBERHOME/dat/leap/parm
are *very* old ones, referring to the original OPLS united atom parameters.
They are *not* OPLS/AA.
Second, in opls_parm.dat, the values you quote are from the wrong nonbonded
section. In way-old Amber formats, a single parm.dat file could have more
than one set of non-bonded parameters. Look for the OPLS section at the
end of opls_parm.dat.
The opls.info file is (I think) pretty verbatim from Bill Jorgensen, to be
used in his programs, not as direct input to Amber. It is provided both
as a definitive reference and for its useful comments. The value given there
is sigma, whereas Amber files use Rmin/2. If you convert 2.96 (sigma) to
Rmin/2 you get 1.6612, as in the Glycam and gaff files.
...hope this helps....dac
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Received on Thu Aug 08 2013 - 19:00:02 PDT
