The file you downloaded, assuming it is not solvated, is a structure
minimized in the gas phase with a dielectric constant that roughly
approximates solvation in water. The "Sander" file you can download
contains complete simulation details (for example, the dielectric
used). I'm saying this just to be certain you know that the bond
angles, lengths, etc., were derived by applying the Glycam force field
in a molecular dynamics minimization: you probably won't find those
precise values in any input file.
The original paper is here:
Kirschner, Karl N., Yongye, Austin B., Tschampel, Sarah M.,
Gonzalez-Outeirino, Jorge, Daniels, Charlisa R., Foley, B. Lachele,
Woods, Robert J. JOURNAL OF COMPUTATIONAL CHEMISTRY Volume: 29
Issue: 4 Pages: 622-655 Published: MAR 2008
We provide periodic updates to the force field, though. It is
appropriate, therefore, if you also provide the name of the exact
parameter file. Since you downloaded the file in September 2010, it
was Glycam_06g.dat. The name of the file is given at the download
page. You should also reference the site where the parameters can be
obtained (
http://glycam.ccrc.uga.edu/ccrc/pages/parameters.html) and
the site where you built the pdb (e.g.
http://glycam.ccrc.uga.edu/ccrc/carbohydrates/cb_newbuilder.jsp). If
you know the date on which you downloaded the file, you can check the
changelog in the documentation on the parameters page to find out
which force field was used.
:-) Lachele
On Tue, Jul 5, 2011 at 1:49 AM, Sushil Mishra <sushilbioinfo.gmail.com> wrote:
> You can have a look in the developer's web-page where they have information
> about citations of GLYCAM force field as well as web-tool Carbohydrate
> Builder. .
> http://glycam.ccrc.uga.edu/ccrc/pages/cite.html
> Hope it helps.
>
> /sushil
>
> On Tue, Jul 5, 2011 at 7:14 AM, subrata paul <paul.subrata34.gmail.com>wrote:
>
>> Dear
>> Amber user
>> I am simulating trehalose and water solution. For trehalose molecule , I
>> downloded a pdb (glycam_9_6_2010_MIN.pdb) from *
>> http://glycam.ccrc.uga.edu/ccrc/pages/3dspt.html
>> *
>> I am using Amber10 with GLYCAM_06 force field. From which reference paper
>> all parameters ( charge , bond, angle, dihedral ) for trehalose are taken
>> by the GLYCAM_06 force field ?
>>
>>
>>
>> thanking you
>> subrata
>> IITG
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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>
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Tue Jul 05 2011 - 07:30:03 PDT
