On Tue, May 8, 2012 at 1:01 PM, rama david <[email protected]> wrote:
> > > 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.... >> >> As the tutorial suggest you can restrain the heavy atoms, but I usually restrain the entire protein during the InflateGro steps (EMs) and let the lipids minimize around it. -Anirban > >> >> All suggestions are welcome >> thank you in advance >> >> >> Rama David . >> >> > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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