[gmx-users] pdb2gmx

Justin A. Lemkul jalemkul at vt.edu
Mon Aug 31 13:19:36 CEST 2009

leila karami wrote:
> there is 1 fatal error in pdb2gmx command about pdb file containing 2 
> separate pdb file (protein:nmr structure, dna: x-ray structure). error 
> :[There were 38 missing atoms in molecule, if you want to use this 
> incomplete topology anyhow, use the option -missing](all of missing 
> atoms are H atom). what do I do instead of -missing option?

If all of the atoms are H, use -ignh and allow pdb2gmx to build in all those 
that are necessary.


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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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