Steven Kirk wrote:
Hello,
I'm using a macromolecule with the OPLS-AA force field, solvated with
SSWM4-DP polarizable water (many thanks to DvS for this). The .itp file
for the polarizable water has a [defaults] line that looks like:
[ defaults ]
LJ Geometric
whereas when the OPLS-AA forcefield .itp files are read in, they contain
a defaults section that looks like this:
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 3 yes 0.5 0.5
and hence grompp complains about two [defaults] sections.
I know comb-rule 3 means geometric averages of LJ parameters, but I'm
wondering about the compatibility of the 'gen-pairs', 'fudgeLJ' and
'fudgeQQ' parameters.
Can anyone suggest a single defaults line that would be compatible with
both of these ? Could I safely use ONLY the OPLS-AA defaults line
without breaking SSWM4-DP?
Many thanks,
Steve Kirk
Apart from just trying it, which I recommend you do, the SW models don't
have any 1-4 interactions so you are safe there. For more involved
molecules this may be a problem.
--
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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