[gmx-users] inositol simulations

[david.evans at ulsop.ac.uk]

Hi,

What happens if you simulate GLCA itself --- does it always go into
the boat as well?

Dave Evans
School of Pharmacy, University of London

---- Message from Shozeb Haider <shozeb at biop.ox.ac.uk> at 2004-11-03
23:39:19 ------
>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
>
>

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