The Glycam06 parameter set should work well. Be sure to get the
latest set. It can be downloaded here:
http://glycam.ccrc.uga.edu/documents/gl_params.jsp
The online web tool will not build a usable cyclic molecule for you,
so you will need to do it manually using some variant of Leap. I
recommend using a graphical version since you will be altering
torsions. The following information should help somewhat:
1] Load in the latest glycam parameter and prep files.
2] Build a linear sequence. Assuming you want seven a-D-glucopyranose
molecules linked in a (1-4) configuration, it would look like:
molecule = sequence { 4GA 4GA 4GA 4GA 4GA 4GA 4GA }
Note that the order of the resides is backwards here from standard
nomenclature -- a fact not immediately obvious upon inspection. In
other words, the first two "4GA" residues are linked together like
this:
molecule.1.O4 -- molecule.2.C1
...and not the other way around, as you would mean if you said
"a-D-Glcp (1-4) a-D-Glcp".
3] Next, you need to set the torsions between the residues so that
they will form a ring. I will leave it up to you to determine which
torsions should go where. It will probably be easiest if you can find
a source in the literature that contains information about the
torsions. You can set the torsions with the "impose" command.
4] Finally, bond the last 4GA to the first one. The command should
look something like:
bond molecule.1.C1 molecule.7.O4
... or, alternately:
bond molecule.7.O4 molecule.1.C1
5] Save the parm and top files.
6] Load the parm/top files into VMD or some similar viewer to ensure
that the molecule you built is the molecule you wanted.
Let me know if that helps, doesn't work, etc.
:-) Lachele
On Fri, May 1, 2009 at 10:51 AM, Rajesh Raju
<Rajesh.Raju.postgrad.manchester.ac.uk> wrote:
> Hi,
>
> Can any one suggest how to get the paramterand coordinate file for beta
> cyclo dextrin. I want to perform MD simulations on beta cyclodextrin.
> Thanking u in advance
>
>
>
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Wed May 20 2009 - 14:02:51 PDT
