[gmx-users] g_confrms_d options

[David van der Spoel]

Arindam Ganguly wrote:
> Hi Gmx-users,
> i am facing this problem i really don;t get it. i am trying to  compare 
> the  rmsd  of  two strucures  and when i  use  g_confrms_ d i  the 
> following  options for the two structures
> 
> Group     0 (      System) has  4276 elements
> Group     1 (     Protein) has  4276 elements
> Group     2 (   Protein-H) has  3260 elements
> Group     3 (     C-alpha) has   388 elements
> Group     4 (    Backbone) has  1164 elements
> Group     5 (   MainChain) has  1556 elements
> Group     6 (MainChain+Cb) has  1932 elements
> Group     7 ( MainChain+H) has  1932 elements
> Group     8 (   SideChain) has  2344 elements
> Group     9 ( SideChain-H) has  1704 elements
> Group    10 (     Protein) has  4276 elements
> 
> 	
> 
> Group     0 (      System) has  1198 elements
> Group     1 (     Protein) has  1053 elements
> Group     2 (   Protein-H) has   802 elements
> Group     3 (     C-alpha) has    96 elements
> Group     4 (    Backbone) has   288 elements
> Group     5 (   MainChain) has   385 elements
> Group     6 (MainChain+Cb) has   478 elements
> Group     7 ( MainChain+H) has   478 elements
> Group     8 (   SideChain) has   575 elements
> Group     9 ( SideChain-H) has   417 elements
> Group    10 ( Prot-Masses) has  1053 elements
> Group    11 ( Non-Protein) has   145 elements
> Group    12 (          NA) has     1 elements
> Group    13 (         HOH) has   144 elements
> Group    14 (       Other) has   145 elements
> Group    15 (     Protein) has  1053 elements
> 
> i am able to calculate all options however for the "C-alpha" it keeps on 
> giving me an error and the error is  "You selected groups with different 
> number of atoms."
> 
> if you look at all other options also have different number of atoms, so 
> howcome i don;t get this error message in other options. is there really 
> problem here or i am missing something. pzl help thanks.
> 
> Arindam Ganguly
> 
It's simply as it says: you're comparing apples and oranges, first 
protein is four times as large. If you want to do sequence alignment 
first, you'll have to use something else.

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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