[gmx-users] inositol simulations

[Shozeb Haider]

Dear Users,

I am simulating inositol (4,5) bis phosphate. I generate the topology
from prodrg server. I compared the parameters (impropers and dihedrals)
for the sugar with those of glucose (GLCA) in the ffgmx.rtp file.
However on running the minimisation and dynamics, the sugar only tends
to adopt the boat conformation. Could any one point me in the direction
where I might be faltering? Initially Prodrg outputed a list of
impropers that did not comply with the GLCA imporpers in the .rtp file.
However, correcting those give the same result i.e. the boat conformation.

Any suggestions would be more than appreciated.

best wishes

Shozeb Haider