[gmx-users] reading Hydrogens from an itp file

[Justin Lemkul]

On Tue, Apr 9, 2013 at 5:19 AM, gromacs query <gromacsquery at gmail.com>wrote:

> Dear All,
>
> I have a pdb file in which has only heavy atoms (means all atoms except
> hydrogen) and a corresponding itp file with all atoms (including
> hydrogens). The heavy atoms in pdb file are in sequence order as in itp
> file.
>
> e.g.
> itp       pdb (no Hydrogens)
> ****     *****
> C1       C1
> H1       C2
> H2       O1
> H3
> C2
> H4
> H5
> O1
>
> With this pdb (missing Hs ) Is there any way to add hydrogens (which are in
> itp file) to write a *.gro file having all heavy and hydrogen atoms?
>
>
Write an .hdb entry and pdb2gmx will do it for you.

-Justin

-- 

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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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