Anthony Cruz wrote:
Hi users:
I have a little question. I found some L-J parameters for heme iron for the
GROMOS87 FF and I want to use it in the GROMOS ff43a1 . The units as appear
in the paper [biophys. J. 1995 (69) p810] A(kJ nm^ -12 mol ^-1) 4.30115e-5
and B (kJ nm^ -6 mol ^ -1) 8.886909e-3. I need to make any changes to the
values there is any convertion factor??
it looks about right, but check the equations in the paper and compare
to those in the manual.
Also I found other L-J parameters [J. Phys. Chem. B 2002 (106) p12031] the
unit for this other are A[(kcal/mol)/A^12] 10389.5 and B[(kcal/mol)/A^6]
288.3 also appear the fallowing equation Vnb(rij) =Aijrij^ -12 - Bijrij ^ -6
with Aij(Bij) the geometric means of Ai and Aj(Bi and Bj). How I can
inplemet this values to use it in the GROMOS ff43a1????
I think is is default, but check the section about combination rules
in the manual.
--
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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