Whenever I use this protocol ,I always get 0 refined pose although the pharmacophore matching is perfect.
Here is a simple trial which I performed today.
1-I used the 1fvv protein and ligand which are found in DS sample folder
2-I autogenerated a pharmacophore using receptor ligand pharmacophore generation module
3-I removed the execluded volumes
4-I run the charmm with pharm.constrain modules using the defaults except that I set conf generation to none as this was the bound conformer
5-The result is always the same whatever the conditions
0 refined pose
I tried these options too but in vain
a) setting the force restraint to lower value
b)setting simulated annealing to none
Please help me out
I tried to use cdocker on the conformer obtained from pharmacophore alignment and set random conformations to 0 and it gave good poses