[gmx-users] Hydrogen atoms type

[Justin A. Lemkul]

Amir Abbasi wrote:
> Hi Dear Users!
> I'm Using MMB to produce initial structures for my simulations.
> This program creating a .pdb file in output.
> The output file containing Hydrogen atoms that are not recognized by 
> gromos53a5.
> I want to edit my pdb file but I can't find anything about "hydrogen 
> types in gromos"!
> any suggestion?
> 

The Gromos force fields are united-atom, so most H atoms are not used.  Aromatic 
hydrogens are type HC and polar hydrogens are type H.

If you're trying to run your structure through pdb2gmx and it's complaining, use 
-ignh and only necessary hydrogens will be built back on.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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