[gmx-users] carbohydrate parameters in ffG53a6
Justin A. Lemkul
jalemkul at vt.edu
Sat Aug 28 20:11:34 CEST 2010
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.
-Justin
> -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
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> <mailto:gmx-users at gromacs.org>>>>
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> <mailto:456742.75700.qm at web8903.mail.in.yahoo.com>>>>
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> 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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