[gmx-users] adding missing hydrogen using pdb2gmx

[Justin Lemkul]

On 10/6/18 1:19 AM, marzieh dehghan wrote:
> Hi
> Dear all
> I want to add missing hydrogen to the related protein structure using
> pdb2gmx, but I don't know how to solve this problem. please let me know how
> to add hydrogen to all residues in the pdb file like the following sample:
>
> ATOM     17  N   LEU A   2      24.961  35.448  12.600  1.00  0.00
> ATOM     18  H   LEU A   2      24.492  36.325  12.498  1.00  0.00
> ATOM     19  CA  LEU A   2      26.417  35.419  12.376  1.00  0.00
> ATOM     20  HA  LEU A   2      26.538  34.909  11.524  1.00  0.00
> ATOM     21  CB  LEU A   2      26.929  36.867  12.209  1.00  0.00
> ATOM     22  HB1 LEU A   2      27.927  36.831  12.158  1.00  0.00
> ATOM     23  HB2 LEU A   2      26.564  37.219  11.347  1.00  0.00
> ATOM     24  CG  LEU A   2      26.545  37.867  13.333  1.00  0.00
> ATOM     25  HG  LEU A   2      25.850  37.419  13.895  1.00  0.00
> ATOM     26  CD1 LEU A   2      27.728  38.220  14.229  1.00  0.00
> ATOM     27 HD11 LEU A   2      27.432  38.864  14.934  1.00  0.00
> ATOM     28 HD12 LEU A   2      28.078  37.389  14.662  1.00  0.00
> ATOM     29 HD13 LEU A   2      28.450  38.638  13.678  1.00  0.00
> ATOM     30  CD2 LEU A   2      25.989  39.165  12.744  1.00  0.00
> ATOM     31 HD21 LEU A   2      25.749  39.792  13.485  1.00  0.00
> ATOM     32 HD22 LEU A   2      26.681  39.589  12.160  1.00  0.00
> ATOM     33 HD23 LEU A   2      25.173  38.963  12.202  1.00  0.00
> ATOM     34  C   LEU A   2      27.204  34.604  13.424  1.00  0.00
> ATOM     35  O   LEU A   2      27.949  33.691  13.068  1.00  0.00
>
>
> I am looking forward to getting your answer

Have you tried actually running pdb2gmx? Part of what it does is 
automatically build missing hydrogens.

-Justin

-- 
==================================================

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

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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