[gmx-users] doubt about the oplsaa topology

Serena Leone sleone at rics.bwh.harvard.edu
Fri Sep 12 23:41:48 CEST 2008

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 

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
(tel)  617-732-8586

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