Re: [gmx-users] the effect of the ligand on each residue

[Justin A. Lemkul]

ahmet yıldırım wrote:
Dear Justin,

Thanks for your reply. Well, to explore the effect of the ligand on protein

g_mindist -f run.xtc -s run.tpr -od mindist.xvg -on numcont.xvg
Select a group: 1
Selected 1: 'Protein'
Select a group: 13
Selected 13: 'LİGAND'

Does this choice make sense?


Whether or not anything makes sense is up to you.  You have to interpret the 
data you get for your system.  The command is sound, so you probably got output. 
 But as for the applicability or whether or not it makes sense to do this 
analysis is, again, entirely up to you.

-Justin


30 Haziran 2011 14:43 tarihinde Justin A. Lemkul <jalem...@vt.edu 
<mailto:jalem...@vt.edu>> yazdı:



    ahmet yıldırım wrote:

        Dear users,

        I want to see the effect of the ligand on each residue using the
        following command:
        g_rmsf -s run.tpr -f run.xtc -od rmsdev.xvg -o rmsf.xvg -res

        Select group(s) for root mean square calculation
        Select a group: ?
        Which group should I choose?


    The group that is most meaningful to you, based on the behavior
    observed in the trajectory.  You can analyze backbone, sidechain, or
    all protein atoms separately.  Several iterations may be
    informative, using several different groups.

    -Justin

    -- 
    ==============================__==========

    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
    <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>

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--
Ahmet YILDIRIM

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

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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