[gmx-users] how to fix alpha carbon atoms

David van der Spoel spoel at xray.bmc.uu.se
Fri Nov 16 20:36:02 CET 2001

On Fri, 16 Nov 2001, David L. Bostick wrote:

>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.
This way you are freezing the motion, i.e. the backbone can not move at
all. This may be too restrictive.
As an alternative you can use position restraints on the C-alpha atoms, in
that case the atoms are coupled to their starting position by a harmonic
spring, but can still move a little. Use genpr to generate position
restraints, and replace those in the .top file with it (at the right
position!). Then check your defines (pdb2gmx produces something with an
#ifdef POSRES
#include "posre.itp"
so if your new file is called posre.itp you don't have to change the itp
file only to change the mdp file line:
define = -DPOSRES

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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