[gmx-users] doubt about the oplsaa topology

[Serena Leone]

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






The information transmitted in this electronic communication is intended only
for the person or entity to whom it is addressed and may contain confidential
and/or privileged material. Any review, retransmission, dissemination or other
use of or taking of any action in reliance upon this information by persons or
entities other than the intended recipient is prohibited. If you received this
information in error, please contact the Compliance HelpLine at 800-856-1983 and
properly dispose of this information.