Hi,
I am trying to simulate a Protein Ligand system. Now, my system has some
non standard residues and I standardized them for AMBER forcefield using
ACPYPE. However, when I assemble the gro files of the Proten generated from
pdb2gmx and the gro files obtained from ACPYPE, I see that they are not
Hi,
The only thing that matters is the order of the molecules, residues and
atoms, and preferably naming. These must match between topology and
coordinates when you eg use grompp. The point of doing an MD simulation is
generally to keep the topology constant while changing the coordinates. So
give
Hi,
Grompp is running successfully without any errors. But my protein and
ligands are very far away from each other. So, what I fear is that the
interactions among them may not be well accounted for by MD simulations.
On Mon, Aug 7, 2017 at 7:53 PM, Mark Abraham
wrote:
> Hi,
>
> The only thing
On 8/7/17 3:01 PM, Souvik Dey wrote:
Hi,
Grompp is running successfully without any errors. But my protein and
ligands are very far away from each other. So, what I fear is that the
interactions among them may not be well accounted for by MD simulations.
If the coordinates that came out of
