[gmx-users] adding a polar Hydrogen atom to pdb file

Justin A. Lemkul jalemkul at vt.edu
Tue Feb 12 15:24:21 CET 2008

Quoting kinshuk at chem.iitb.ac.in:

> Hi all,
> i have to edit a pdb file that will have all polar hydrogens & non polar
> hydrogens.while dealing with pdb2gmx commands it only adds polar hydrogens
> not non polar hydrogens.So how to get the pdb files having polar as well
> as non polar atoms in a pdb files.

Use an all-atom force field, like OPLS-AA or AMBER.  Or if you just want the
.pdb file, check out protonate -h.


>  i will be thankful for any positive response.
> Kinshuk
> IIT-Bombay
> India
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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