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

[Justin A. Lemkul]

Stefano Meliga wrote:
> 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 
> created.
> 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.
> 
> 

Choose an all-atom force field with pdb2gmx (i.e., OPLS-AA).  The hydrogens will 
be added by pdb2gmx.

-Justin

> Thank you for your help,
> 
> Stefano
> 
> 
> 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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>>
> 

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

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

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