[gmx-users] doubt about the oplsaa topology
sleone at rics.bwh.harvard.edu
Fri Sep 12 23:41:48 CEST 2008
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
thanks a lot...
great day to all...
Serena Leone, Ph.D.
Brigham and Women's Hospital
Harvard Medical School
Channing Laboratory EBRC 609
221 Longwood Avenue
Boston, MA 02115
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