Running a simulation with a protein and a sugar

From: pellegrini (pellegrini_at_ill.fr)
Date: Thu Aug 27 2009 - 04:06:48 CDT

Hello everybody,

I know that this kind of questions has already been posted here but I
did not really understand the answers ...

I have a structure made of a protein, a sugar and some calciums ions.
For the protein and the calcium no problem
for generating the PSF but I went into troubles with the sugar because
its building block is not parametrized. I managed
to get the parameters for the sugar using glycam but those parameters
are in Amber format.

So I end up with the following settings:

    -PSF file for protein and calcium
    -top and crd files for the sugar

would you have any idea about how to setup a simulation (e.g. a
minimization) out of this ?
Is there a simple way to get a PSF file for the sugar out of the amber
files ?

thank you very much for your help

best regards

Eric

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