[gmx-users] Adding Hydrogens by pdb2gmx

[James Starlight]

Its very unclear for me because after pdb2gmx -f 1.pdb -o conf.gro -ignh
with gromos force field

I've checked conf.gro by VMD and this structure didnt contains any
hydrogens ;o

James

2011/10/31 Justin A. Lemkul <jalemkul at vt.edu>

>
>
> James Starlight wrote:
>
>> Dear Gromacs Users!
>>
>> I could not find how I can add missing hydrogens after their removing by
>> pdb2gmx -ignh.
>>
>> I have modified structure of my protein after editing by some soft and I
>> removed all hydrogens but now I want to add it back in accordance with
>> gromos ff topology
>>
>> How I can do it ?
>>
>>
> They are removed and rebuilt entirely by pdb2gmx in accordance with the
> instructions found in the .hdb file.  If there are no hydrogens in the
> input, then -ignh is irrelevant.
>
> -Justin
>
> --
> ==============================**==========
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> Justin A. Lemkul
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> ICTAS Doctoral Scholar
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> Department of Biochemistry
> Virginia Tech
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> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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