Re: [gmx-users] carbohydrate parameters in ffG53a6

[Justin A. Lemkul]

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.

-Justin

I hope it would be useful for you.

Rasoul
On Wed, Aug 18, 2010 at 6:45 PM, Justin A. Lemkul <jalem...@vt.edu 
<mailto:jalem...@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 <parichitamajum...@yahoo.co.in
        <mailto:parichitamajum...@yahoo.co.in>
        <mailto:parichitamajum...@yahoo.co.in
        <mailto:parichitamajum...@yahoo.co.in>>

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        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 <jianhuit...@gmail.com
        <mailto:jianhuit...@gmail.com> <mailto:jianhuit...@gmail.com
        <mailto:jianhuit...@gmail.com>>> wrote:


        From: Jianhui Tian <jianhuit...@gmail.com
        <mailto:jianhuit...@gmail.com> <mailto:jianhuit...@gmail.com
        <mailto:jianhuit...@gmail.com>>>

        Subject: [gmx-users] carbohydrate parameters in ffG53a6
        To: gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>
        <mailto:gmx-users@gromacs.org <mailto:gmx-users@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> | (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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