On 11/13/17 3:00 AM, Ahmet Yildirim wrote:
Sorry. The pymol and GROMACS give the same results for every three target
dihedrals. The updated results are here:
https://www.dropbox.com/s/7qgn7qa4rf2yc14/dih.pdf?dl=0
The results show that the average dihedrals are almost the same in both the
Sorry. The pymol and GROMACS give the same results for every three target
dihedrals. The updated results are here:
https://www.dropbox.com/s/7qgn7qa4rf2yc14/dih.pdf?dl=0
The results show that the average dihedrals are almost the same in both the
state A and state B for both [dihedrals] or
Hi,
Let me take that in reverse order:
>
> Note that choosing appropriate atoms to apply restraints is not a trivial
> matter, and results can vary depending on the choices made.
>
I know.
I doubt there's a bug. I tested this feature a lot myself and have used it.
> How different are the
On 11/10/17 11:59 PM, Ahmet Yildirim wrote:
Hi,
Just tested it. The [ dihedral_restraints ] didn't help. The RMSD of the
ligand is the same when the [ dihedral_restraints ] or [ dihedrals ] is
used at end of the complex topology file. This is a bug?
I doubt there's a bug. I tested this
Hi,
Just tested it. The [ dihedral_restraints ] didn't help. The RMSD of the
ligand is the same when the [ dihedral_restraints ] or [ dihedrals ] is
used at end of the complex topology file. This is a bug?
>From my first mail:
> I think [ dihedral_restraints ] will be the same as [ dihedrals ]
On 11/10/17 2:21 PM, Ahmet Yildirim wrote:
Dear users,
I add the following [ intermolecular_interactions ] section into the
topology file of protein-ligand complex for free energy calculations.
Unfortunately this setting doesn't provide me what I want in the decoupled
state. The ligand in the
Dear users,
I add the following [ intermolecular_interactions ] section into the
topology file of protein-ligand complex for free energy calculations.
Unfortunately this setting doesn't provide me what I want in the decoupled
state. The ligand in the decoupled state is very mobile compared to the
