On 9/4/12 11:21 AM, [email protected] 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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