[gmx-users] make_ndx problem

[Xavier Periole]

On 7 May 2008 07:10:11 -0000
  "minnale " <minnale_gnos at rediffmail.com> wrote:
>  
> Hi all,
> it may be trivial question 
> My protien contain nearly 200 residues, I want plot RMSD for 45 to 90 
>residues , So I made make_ndx file also, but I am doubting that what i have I 
>done whether right ot wrong? 
> I have selcted 
> 1 | r 45-90 1 = protein , the way I have selected is correct or I have to 
>select 
> 3 | r 45-90 3 = C-alpha
This won't give you what you want.
you have to use
1 & r 45-90 : all protein atoms whithin residues 45-90
or 3 & 45-90 : all Ca atoms within residue 45-90
the sign "|" adds up the two groups
the sign "&" take the intersection between the groups

you could do the check yourself, by editing the output index
it and verify that the atom numbers given are or not what you want.
> Pls tell me
> Thanks in advance

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XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
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