[gmx-users] Re: Justin lipid-position restraine
reach.anirban.ghosh at gmail.com
Tue May 8 10:27:43 CEST 2012
On Tue, May 8, 2012 at 1:01 PM, rama david <ramadavidgroup at gmail.com> wrote:
> 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......
>> 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.
>> All suggestions are welcome
>> thank you in advance
>> Rama David .
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