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

[Justin Lemkul]

On 1/22/18 5:58 AM, Seera Suryanarayana wrote:
> 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.

Have you tried looking at the examples provided by make_ndx? Type "help" 
at the prompt and it will show you how to use the program. It's very simple.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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jalemkul at vt.edu | (540) 231-3129
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