AMBER Archive (2009)

Subject: Re: [AMBER] Cyclodextrin forcefield

From: Lachele Foley (Lists) (lf.list_at_gmail.com)
Date: Fri May 01 2009 - 10:23:37 CDT

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_at_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
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> 

-- 
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA

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