Check out ffoplsaanb.itp to see which name (opls_XXX) corresponds to which
bond type (ie. what you are seeing in ffoplsaabon.itp)
Tom
--On Friday, September 12, 2008 17:41:48 -0400 Serena Leone
[EMAIL PROTECTED] wrote:
Hello all,
I am trying to build the topology for an oligosaccharide to be used,
together with a peptide, in a simulation with oplsaa (apparently, from
the discussions in the last days, this should be the best choice...).
Now, I had a .top from prodrg that I previously modified and used, and I
was starting rewriting on it the new .top for the oplsaa. After renaming
all the atoms according to the ffoplsaa.atp, ( i will figure out later
how to include the missing non polar Hs), i wanted to check that all the
bonds in this molecule were described in the ffoplsaabon.itp (i have
sulfate groups) BUT, when I opened the ffoplsaabon.itp, I noticed that
the atom names don't correspond to the types described in the .atp
(opls_n), but more likely to the names in any other gro force field. I'm
confused... anybody can explain me this contradiction?
thanks a lot...
great day to all...
serena
--
Serena Leone, Ph.D.
Brigham and Women's Hospital
Harvard Medical School
Channing Laboratory EBRC 609
221 Longwood Avenue
Boston, MA 02115
(tel) 617-732-8586
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