[gmx-users] generating gro files using pdb2gmx without adding hydrogen

David van der Spoel spoel at xray.bmc.uu.se
Thu May 19 09:53:02 CEST 2005

On Thu, 2005-05-19 at 07:06 +0000, balamurugan r wrote:
>   Dear Sir,
>             I have to run MD simulation for a protein under certain pH
> and i have added the hydrogens to the pdb file accordingly using
> BUILDER module in InsightII.  
>           Now i have the pdb file with required hydrogens added and i
> want to generate a gro file but i dont want pdb2gmx to add further
> hydrogens to my pdb file.
>           What are my options?
This will only work if the order of the atoms is correct (according to
gromacs standards).

The alternative is to have gromacs specifically protonate (or not) each
residue in your protein, by using the -inter flag.

> Balamurugan
> Bioinformatics Centre
> Pondicherry University
> India
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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