[gmx-users] adding hydrogens to protein with pdb2gmx

Justin Lemkul jalemkul at vt.edu
Tue Sep 4 17:23:44 CEST 2012

On 9/4/12 11:21 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
> Hi everybody,
> when I want the program "pdb2gmx" only to create a topology file but not
> to change anything at the protein. Not even adding hydrogen atoms to the
> protein.
> Because my protein already has hydrogen atoms. I only added one residue
> and I want to minimize this residue now.
> Do I have to call it like this:
> pdb2gmx -f inputProtein.pdb -o outputProtein.gro -p protein.top -i
> posre.itp  -water none -ff amber03 -ignh
> Is that right?

No.  The use of -ignh tells pdb2gmx to ignore any input hydrogens and build its 
own.  That is the exact opposite of what you are trying to do.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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