[gmx-users] adding hydrogens to protein with pdb2gmx

reisingere at rostlab.informatik.tu-muenchen.de reisingere at rostlab.informatik.tu-muenchen.de
Tue Sep 4 17:32:41 CEST 2012

But the rest of the command was correct?

Since I only want to minimize the phosphates which I added to the protein
I want to use the freeze option to make sure that the other residues will
not change.
But how can I say gromacs that it shell make an exception and do not
freeze the phosphate of the residues where I added the phosphate?

Thank you!!

> 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
> --
> ========================================
> 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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