On 4/28/20 5:08 AM, Elham Taghikhani wrote:
Hi
As you said I checked my structure for any bad contact, but the close atoms are
part of the protein so I can't delete them to minimize the structure. And water
molecules are not that much close to make bad contact with the atom.
And the atom
Hi
As you said I checked my structure for any bad contact, but the close atoms are
part of the protein so I can't delete them to minimize the structure. And water
molecules are not that much close to make bad contact with the atom.
And the atom which errored during minimization it's the atom
On 4/19/20 4:38 PM, Elham Taghikhani wrote:
Thank you
I corrected the mdp file. As you said I opened my gro file in VMD but I didn't
notice any bad contact around the atom.
Could you explain how can I observe bad contacts in the structure?
Calculate interatomic distances and look for
Thank you
I corrected the mdp file. As you said I opened my gro file in VMD but I didn't
notice any bad contact around the atom.
Could you explain how can I observe bad contacts in the structure?
I even tried the different box size but it didn't work.
Both ligand and protein are ok with
On 4/19/20 2:43 PM, Elham Taghikhani wrote:
Hi
I am simulating a protein-ligand system, using oplss force field but i got
this error during minimization.
Steepest Descents:
Tolerance (Fmax) = 1.0e+03
Number of steps = 5
Step= 0, Dmax= 1.0e-02 nm, Epot=
Hi
I am simulating a protein-ligand system, using oplss force field but i got
this error during minimization.
Steepest Descents:
Tolerance (Fmax) = 1.0e+03
Number of steps = 5
Step= 0, Dmax= 1.0e-02 nm, Epot= 1.27151e+33 Fmax= 4.76291e+07, atom= 1996
Segmentation
