On Tue, May 8, 2012 at 1:01 PM, rama david ramadavidgr...@gmail.com wrote:
On Tue, May 8, 2012 at 1:00 PM, rama david ramadavidgr...@gmail.comwrote:
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 10 10 10
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) has16 elements
Group 4 ( Backbone) has48 elements
Group 5 ( MainChain) has64 elements
Group 6 ( MainChain+Cb) has78 elements
Group 7 (MainChain+H) has81 elements
Group 8 ( SideChain) has57 elements
Group 9 (SideChain-H) has45 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 .
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