[gmx-users] Regarding indexing the atom labelled same in peptide

[Mark Abraham]

Hi,

The "1" selects the first index group, which is the whole peptide. If you
want to select the first residue, you have to use some other syntax.

Mark

On Tue, Aug 22, 2017 at 6:50 PM Dilip H N <cy16f01.dilip at nitk.edu.in> wrote:

> Hello,
> I have a Diglycine peptide in .gro file as:-
> 1GLY      N    1   1.312   0.940   1.100  0.5173  0.1852  0.2665
> 1GLY     H1    2   1.375   1.015   1.064  0.3308 -0.2009 -0.8897
> 1GLY     H2    3   1.376   0.860   1.115  2.0625  0.7372 -2.9245
> 1GLY     H3    4   1.242   0.907   1.031  0.2385  0.6317  0.3326
> 1GLY     CA    5   1.240   0.963   1.228  0.3801 -0.0854  0.2381
> 1GLY    HA1    6   1.155   0.898   1.233  1.2980 -1.3807 -0.5280
> 1GLY    HA2    7   1.321   0.963   1.300 -1.1296 -1.6137  1.9682
> 1GLY      C      8   1.185   1.101   1.232  0.0318 -0.2122 -0.1516
> 1GLY      O    9   1.171   1.174   1.133  0.1199  0.2166  0.1513
> 2GLY      N   10   1.148   1.148   1.352 -1.0777 -0.3721 -0.4264
> 2GLY     HN   11   1.142   1.091   1.434 -0.1054  0.0667 -0.0362
> 2GLY     CA   12   1.092   1.277   1.377  0.5476  0.2162  0.2355
> 2GLY    HA1   13   1.170   1.351   1.365  0.3836  0.3441 -0.0427
> 2GLY    HA2   14   1.012   1.294   1.306 -0.5941  1.1037  1.7136
> 2GLY      C   15   1.031   1.298   1.514  0.2354 -0.4348  0.1971
> 2GLY    OT1   16   0.923   1.238   1.541  0.2601 -0.2386  0.7420
> 2GLY    OT2   17   1.091   1.369   1.598  0.1878 -0.0650 -0.0813
>
> So now i want to index of the Nitrogen (N) of 1GLY only, but not N of
> 2GLY...
>
> I tried the the following command as:-
> gmx make_ndx -f abc.gro -o def.ndx
> 1 & a N
>
> But it is giving  2 Protein_&_N  : 2 atoms
> which is taking the N of 2GLY too into consideration....which i don't
> required, I need the N of ...1GLY only....
>
> So what is the correct command for this..??
>
> Thank you...
>
>
>
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
>
>
>
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