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

[Dilip H N]

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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