[gmx-users] Re: Justin lipid-position restraine

[rama david]

On Tue, May 8, 2012 at 1:00 PM, rama david <ramadavidgroup at gmail.com> 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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