[gmx-users] RMSD of sidechain

[Anton Feenstra]

Tanos wrote:

>    Hi folks,
>    I am facing a problem to generate the spatial RMSD graphycs of the 
> sidechain of my protein !!!!!
>        I  first run  "g_rmsf -n index.ndx -s protein_md.tpr -f 
> protein_md.trr -o rmsdspatial.xvg -res", then I choose either the option 
> sidechain (8) or the option sidechain - H(9) in the index file. In both 
> cases the graphyc generated does not show that points where the curve 
> goes to zero, corresponding to the glicines (that do not have 
> sidechain). What am I doing wrong ??? Can someone help-me ???

Most likely, there will not be a point for the glycine. You could check your .xvg
file by hand to see if the glycine residue numbers actually occur in the file.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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