AMBER Archive (2009)

Subject: Re: [AMBER] Cyclodextrin forcefield

From: Rajesh Raju (Rajesh.Raju_at_postgrad.manchester.ac.uk)
Date: Fri May 01 2009 - 12:21:21 CDT

Hi Lachele Foley,

Thank you very much for ur help...

Thanks

Quoting "Lachele Foley (Lists)" <lf.list_at_gmail.com>:

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