[gmx-users] how to fix alpha carbon atoms

David L. Bostick dbostick at physics.unc.edu
Fri Nov 16 19:45:40 CET 2001


You can make an index file using make_ndx which contains the groups you
wish to restrain.  In this case, the c-alpha backbone.  Then you can use
the options 

freezegrps = BACKBONE
freezedim = Y Y Y

I think that either the C-alpha or entirely, the backbone of a protein
are standard groups so you may not even have to create an index file for
input to grompp.

David Bostick					Office: 262 Venable Hall
Dept. of Physics and Astronomy			Phone:  (919)962-0165 
Program in Molecular and Cellular Biophysics 
UNC-Chapel Hill					
CB #3255 Phillips Hall				dbostick at physics.unc.edu	
Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick	

On Fri, 16 Nov 2001, Geraudis Mustelier wrote:

> Dear gromac's users
> I am interested in the use of gromacs for to refine a model of protein,
> obtained with modeling by homology. But I want to fix the alpha carbon
> atoms, so, only the side-chain must to change in the molecular dynamic
> computations.
> How I can do this?
> Where and how to say to gromacs that restrict the movement or to fix the
> coordinates of alpha carbons (or backbone) during the molecular dynamic
> simulations?
> Please, I hope hearing from somebody as soon as possible
> ====================================================================
>  MSc. Geraudis Mustelier-Portuondo
>  Center of Molecular Immunology
>  Calle 216 esq. A 15, Atabey, Playa
>  A. Postal 16040, Havana 11600, CUBA
>  email: gera at ict.cim.sld.cu
>  http://bioinfo.cim.sld.cu
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>  Fax: 53-7-335049
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