[gmx-users] carbohydrate parameters in ffG53a6
Rasoul
nasiri1355 at gmail.com
Sat Aug 28 20:34:55 CEST 2010
On Sat, Aug 28, 2010 at 8:11 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Rasoul wrote:
>
>
>>
>> On Thu, Aug 19, 2010 at 1:02 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>>
>>
>> Rasoul wrote:
>>
>> 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
>>
>>
>> Mixing and matching force field parameters is a very bad idea. To
>> have a valid
>> physical model, parameters should be derived in compatible ways.
>>
>> It has good consistency with Amber FF :J Comput Chem 29: 622–655, 2008.
>>
>>
> That's exactly what it was designed to do, which I don't question. But the
> OP was attempting to develop united-atom parameters for use with Gromos96
> 53A6. For clarity, I pointed out that mixing GLYCAM and 53A6 is an incorrect
> notion.
>
> Amber and Glycam FF can be imported to Gromacs and this method I think has
a more lower artificiality.
-Justin
>
Rasoul
>
> -Justin
>>
>
>> Rasoul
>>
>> 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 <mailto:jalemkul at vt.edu>
>> <mailto:jalemkul at vt.edu <mailto: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>
>> <mailto:parichitamajumdar at yahoo.co.in
>> <mailto:parichitamajumdar at yahoo.co.in>>
>> <mailto:parichitamajumdar at yahoo.co.in
>> <mailto:parichitamajumdar at yahoo.co.in>
>> <mailto: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>
>> <mailto:gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>> <mailto:gmx-users at gromacs.org
>>
>> <mailto:gmx-users at gromacs.org>
>>
>> <mailto:gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>>>>
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>> <mailto:456742.75700.qm at web8903.mail.in.yahoo.com>
>> <mailto:456742.75700.qm at web8903.mail.in.yahoo.com
>> <mailto:456742.75700.qm at web8903.mail.in.yahoo.com>>
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>> <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>
>> <mailto:jianhuitian at gmail.com
>> <mailto:jianhuitian at gmail.com>> <mailto:jianhuitian at gmail.com
>>
>> <mailto:jianhuitian at gmail.com>
>>
>> <mailto:jianhuitian at gmail.com
>> <mailto:jianhuitian at gmail.com>>>> wrote:
>>
>>
>> From: Jianhui Tian <jianhuitian at gmail.com
>> <mailto:jianhuitian at gmail.com>
>> <mailto:jianhuitian at gmail.com
>> <mailto:jianhuitian at gmail.com>> <mailto:jianhuitian at gmail.com
>>
>> <mailto:jianhuitian at gmail.com>
>> <mailto: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>
>> <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
>> <mailto:gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org> <mailto: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 <http://vt.edu> <http://vt.edu> | (540)
>>
>> 231-9080
>>
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
>>
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>>
>> -- ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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>>
> --
> ========================================
>
> 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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