Dear Yujie Liu,
Can I clarify your suggestions?
copy gly.gro into protein.gro and changed the number of atoms:
) After running "gmx insert-molecules -ci gly.gro -nmol 10 -f
protein_newbox.gro -o protein_glycine.gro",
the "protein_glycine.gro" already contains both protein residues and glycine
But what if the coordinates do not match? I mean Glycine may not have the
same coordinates after.
On Mon, Aug 7, 2017 at 2:48 PM, yujie liu wrote:
>
> The .top file of protein has included itself all parameters, so now you
> only copy gly.gro into protein.gro and changed
Dear Gromacs,
I am doing a MD for a protein with glycines.
For glycine, I use
) gmx pdb2gmx -f gly_clean.pdb -o gly.gro -water spce -inter
and got
) gly.gro
) posre_gly.itp
) topol_gly.top
For protein, I use
) gmx pdb2gmx -f protein.pdb -o protein_processed.gro -water spce -inter -ignh