[gmx-users] doubt about the oplsaa topology

TJ Piggot t.piggot at bristol.ac.uk
Sat Sep 13 03:00:43 CEST 2008

Check out ffoplsaanb.itp to see which name (opls_XXX) corresponds to which 
bond type (ie. what you are seeing in ffoplsaabon.itp)


--On Friday, September 12, 2008 17:41:48 -0400 Serena Leone 
<sleone at rics.bwh.harvard.edu> 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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TJ Piggot
t.piggot at bristol.ac.uk
University of Bristol, UK.

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