[gmx-users] adding hydrogens to protein with pdb2gmx

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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