[gmx-users] Hydrogen bonds for particular residue during simulations.

[Seera Suryanarayana]

Dear gromacs users,

I have done simulations of 20 residue length of peptide for 100ns. I want
to find hydrogen bonds for residue GLU-7.  The topology information for
this residue as follow.

; residue   7 GLU rtp GLU  q -1.0
   121   opls_238      7    GLU      N     39       -0.5    14.0067   ;
qtot 4.5
   122   opls_241      7    GLU      H     39        0.3      1.008   ;
qtot 4.8
   123  opls_224B      7    GLU     CA     39       0.14     12.011   ;
qtot 4.94
   124   opls_140      7    GLU     HA     39       0.06      1.008   ;
qtot 5
   125   opls_136      7    GLU     CB     40      -0.12     12.011   ;
qtot 4.88
   126   opls_140      7    GLU    HB1     40       0.06      1.008   ;
qtot 4.94
   127   opls_140      7    GLU    HB2     40       0.06      1.008   ;
qtot 5
   128   opls_274      7    GLU     CG     41      -0.22     12.011   ;
qtot 4.78
   129   opls_140      7    GLU    HG1     41       0.06      1.008   ;
qtot 4.84
   130   opls_140      7    GLU    HG2     41       0.06      1.008   ;
qtot 4.9
   131   opls_271      7    GLU     CD     42        0.7     12.011   ;
qtot 5.6
   132   opls_272      7    GLU    OE1     42       -0.8    15.9994   ;
qtot 4.8
   133   opls_272      7    GLU    OE2     42       -0.8    15.9994   ;
qtot 4
   134   opls_235      7    GLU      C     43        0.5     12.011   ;
qtot 4.5
   135   opls_236      7    GLU      O     43       -0.5    15.9994   ;
qtot 4

Kindly suggest me how to create index file for this residue.


Thanks in advance
Surya
Graduate student
India.