[gmx-users] adding non-polar hydrogens - incompatibility of pdb2gmx and grompp

Stefano Meliga smeliga at gmail.com
Mon May 18 12:17:56 CEST 2009

Protonate does the job of adding all of the hydrogens but non-polar 
hydrogens are not recognised by pdb2gmx so that the topology file isn't 
Apparently grompp needs the *.top file in input (It says "Input/Output 
error upon giving only the *.gro file in input).
Does this mean that I can't run an MD simulation with a molecule with 
non-polar hydrogens.

Thank you for your help,


Justin A. Lemkul ha scritto:
> Stefano Meliga wrote:
>> Hello,
>> I would like to add non-polar hydrogens as well as the polar ones.
>> Does anybody know if that is possible?
>> I haven't found any related option of the function pdb2gmx.
> protonate -h
> -Justin
>> Thanks,
>> Stefano.
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