Re: create inositol molecule

From: dimka (
Date: Thu Dec 04 2008 - 12:11:20 CST

I've parameterized the PIP2 lipid (phosphoinositide 4,5
bis-phosphate), so if that's the molecule you're looking for let me
know and i'll send you the appropriate topology/coordinates for it.


On Wed, Dec 3, 2008 at 11:48 AM, <> wrote:
> Dear NAMD users and developers,
> I'm trying to build inositol molecule with psfgen. The problem is that I
> don't have a topology definitions for this molecule so I tried to use the
> existing definitions for some cyclic carbohydrate molecules. I'm getting a
> cyclic molecule (chair conformation) but on some carbons I get a strange
> angles for OH. In addition, when I try to change this angles I get nothing.
> I have already read the information about the structure of topology file and
> parameters that specified in the topology file but I still can't build the
> proper structure of needed stereoisomer. I would appreciate it very much if
> someone could help me with this problem. In addition I would like to know if
> I can use the existing definitions for some carbohydrate molecule (4C1
> alpha-D-glucopyranose monomer) in order to build inositol.
> Thank you very much.

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