[gmx-users] pdb2gmx

Justin A. Lemkul jalemkul at vt.edu
Mon Aug 31 12:44:34 CEST 2009

leila karami wrote:
> What is difference between –ignh and –missing option in pdb2gmx command?

Using -ignh allows pdb2gmx to ignore any hydrogen atoms in the input, usually in 
the case of an NMR structure, to properly name and assign those that are 
necessary in the output, processed, structure.

Using -missing is generally a bad idea.  It allows a topology to be built when 
not all of the necessary atoms are present in the input structure file (i.e., 
MISSING remarks in the .pdb file).  If you use such a topology, your results 
will be nonsense.


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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


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