On Tue, May 8, 2012 at 1:00 PM, rama david <[email protected]> wrote:
> Hi Gromacs user, > I am doing the justin tutorial on lipid posted on link...... > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html > > I am following the tutorial very carefully ... > As mentioned in the tutorial I need to generate strong position > restrained on > proteins heavy atoms to ensure that position of atom does not change > during EM > (Energy Minimisation ) > My command line is as follow ..... > > genrestr -f KALP_newbox.gro -o strong_posre.itp -fc 100000 100000 100000 > > > > Reading structure file > Select group to position restrain > Group 0 ( System) has 138 elements > Group 1 ( Protein) has 138 elements > Group 2 ( Protein-H) has 109 elements > Group 3 ( C-alpha) has 16 elements > Group 4 ( Backbone) has 48 elements > Group 5 ( MainChain) has 64 elements > Group 6 ( MainChain+Cb) has 78 elements > Group 7 ( MainChain+H) has 81 elements > Group 8 ( SideChain) has 57 elements > Group 9 ( SideChain-H) has 45 elements > Select a group: > > > > I am using Gromacs 4.5.4 > > Generally position restrain is applied on backbone of protein > So I choose backbone (4) > > Is it right or I have to choose the group protein(138 elements) to apply > position restraine on all protein atoms.... > > > > All suggestions are welcome > thank you in advance > > > Rama David . > >
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