Re: [gmx-users] How to break a disulfide bond ???

[Justin A. Lemkul]

Venkat Reddy wrote:
Hai !
 
with "pdb2gmx -ss", i can select the ss bonds. But after that, how to 
break a particular ss bond (not all).

You cannot break or re-form bonds under classical mechanics (standard MD).

-Justin

     Thank you
 

On Fri, Mar 6, 2009 at 11:01 AM, sharada <shar...@ccmb.res.in 
<mailto:shar...@ccmb.res.in>> wrote:


    pdb2gmx -h 

    sharada


    */-- Original Message --/*
    From: Venkat Reddy <venkat...@gmail.com <mailto:venkat...@gmail.com>>
    To: Discussion list for GROMACS users <gmx-users@gromacs.org
    <mailto:gmx-users@gromacs.org>>
    Date: Fri, 6 Mar 2009 10:50:24 +0530
    Subject: [gmx-users] How to break a disulfide bond ???

    Hai Every one ! Is it possible to break a disulfide bridge using
    gromacs ?????If so,Can anybody suggest me, how to do it???

    Thanks for ur valuable time

    With best wishes
    Venkat Reddy Chirasani
    M.Tech Bioinformatics
    UNIVERSITY OF HYDERABAD
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--
Venkat Reddy Chirasani
M.Tech Bioinformatics
UNIVERSITY OF HYDERABAD


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--
========================================

Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
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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