[gmx-users] carbohydrate parameters in ffG53a6

[Rasoul]

For the sugar parameters you can use Glycam parameters
http://glycam.ccrc.uga.edu/documents/gl_params.jsp
After with specific script it can be convert to Gromac readable file:
http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Other_software

I hope it would be useful for you.

Rasoul
On Wed, Aug 18, 2010 at 6:45 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Jianhui Tian wrote:
>
>> Hi Parichita,
>>
>> Thanks for the suggestion. However, the question is what parameters from
>> ffG53a6 can be used for not included sugars or glycolipid. I guess you can
>> not simply use the charge, angle and dihedral values based on the atom types
>> from 53a6.
>>
>>
> Gromos building blocks are quite transferable between different molecules.
> Compare a few sugars - the parameters are nearly identical.  That is one of
> the central features of this particular force field, that functional group
> charges should be as versatile as possible.
>
> As for the lipids, there are new versions of 53A6 (which I believe have
> been uploaded to the Gromacs site) that perform substantially better than
> the built-in parameters.  The long acyl chains are not particularly accurate
> in the default 53A6.
>
> -Justin
>
>  Jianhui
>>
>> Date: Wed, 18 Aug 2010 16:18:49 +0530 (IST)
>> From: parichita parichita <parichitamajumdar at yahoo.co.in <mailto:
>> parichitamajumdar at yahoo.co.in>
>>
>>  >
>> Subject: Re: [gmx-users] carbohydrate parameters in ffG53a6
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org <mailto:
>> gmx-users at gromacs.org>>
>> Message-ID: <456742.75700.qm at web8903.mail.in.yahoo.com <mailto:
>> 456742.75700.qm at web8903.mail.in.yahoo.com>>
>>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Hi Jianhui,
>>  For your sugar part you can use PRODRG, which will convert coordinates
>> for small molecules in PDB format (or simple text structures) to the
>> following topology formats: GROMOS, GROMACS and  from literature if you can
>> find out the parameters of ffG53a6 force field,  then you can correct the
>> charge, angle and dihedral values that you are collected from the PRODRG.
>> Hope this will help you.
>> Regards...
>> Parichita...........
>>
>>
>>
>> Parichita Mazumder Research Fellow
>> C/O Dr. Chaitali Mukhopadhayay
>> Department of Chemistry
>> University of Calcutta
>> 92,A P C Road
>> Kolkata-700009
>> India.
>>
>> --- On Wed, 18/8/10, Jianhui Tian <jianhuitian at gmail.com <mailto:
>> jianhuitian at gmail.com>> wrote:
>>
>>
>> From: Jianhui Tian <jianhuitian at gmail.com <mailto:jianhuitian at gmail.com>>
>>
>> Subject: [gmx-users] carbohydrate parameters in ffG53a6
>> To: gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
>>
>> Date: Wednesday, 18 August, 2010, 10:16 AM
>>
>>
>> Hi,
>>
>> I want to do some simulations about carbohydrates and glycolipid. In the
>> ffG53a6.rtp file, I just see limited parameters for carbohydrate, like
>> monosaccharide Glucose, Mannose and Galactose. What parameters can be used
>> for others like arabinose? Also, is there any parameters available in the
>> Gromacs force field for glycolipid?
>>
>> Jianhui
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
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