One more thing when I load the prmtop file and then mdcrd file in the vmd
it showed nothing.
Kindly guide whats the problem here thanks
On Wed, Sep 20, 2017 at 9:46 PM, Rana Rehan Khalid <rrkhalid.umich.edu>
wrote:
> I have protein that consist of bay ligand. I follow the antechamber
> tutorial for protein ligand. I extract the ligand and reduced it after that
> I produced mol2 file of ligand then by using AM1-BCC charge model.
> Then i produced frcmod file my ligand frcmod file have no missing
> parameter for bond angle and dihedral. It have 7 missing parameters for
> improper. I also attached the frcmod file kindly check and guide if it is
> right.
>
> Then i use this script for producing prmtop and inpcrd for ligand (non
> standred residue)
>
> then i prepared the prmtop and inpcrd file for protein complex. BUT this
> file work for NBT=0, not work for periodic boundary conditions. How I can
> make it workable to run periodic boundary simulation because i want to
> compare this simulation with other simulation by employing similar flag
> commands.
>
> Kindly guide
>
> Thanks
>
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Received on Wed Sep 20 2017 - 10:00:05 PDT
