Hi Dr. Eastman,

That's solved the problem. I thought I had converted all the quantities from the TINKER units to OpenMM units, but clearly had missed these two. That was a stupid mistake.

Thanks a lot!

The input pdb file is here:

https://drive.google.com/open?id=0B9osC ... kotMUp0Wlk The lig.xml which has the parameters for the ligand is in https://drive.google.com/open?id=0B9osC ... UIxZ1pBQk0

Thanks.

Hi Dr. Eastman, You're right, there was in issue with the numbering. But on fixing that, after the minimization, the RMS between the protein before and after minimization is only 0.002. Also, assuming that that minimization has occurred correctly, when I now take my output of minimization as the inp...

Hi Dr. Eastman, I tried using the CONECT keyword and providing the connectivities at the bottom of the PDB file before I tried this convoluted approach, but that still gave me the same ValueError: No template found for residue 254 (LIG). The set of atoms matches LIG, but the bonds are different . er...

Hi, I am trying to simulate a system of protein + ligand using the AMOEBA force field in OpenMM 7. I have the AMOEBA parameters for the ligand, and I have previously simulated the system in TINKER. I am now trying to do the simulation in OpenMM. I created a new AMOEBA parameter file from the existin...

Hi Dr. Eastman,

I've created a pull request.

Thanks.

Saurabh

Hi Dr. Eastman, I've implemented my own functions to get both, the permanent and total dipoles in a source version I had forked from the github repo when it was OpenMM 6.3. I am now using OpenMM 7 (from conda, not from source) and want to use these functions in that version as well. I've checked the...

Hi Dr. Eastman,

Running the job in OpenMM 7.0.1, it completed without any error. Maybe it is something specific to the 6.3 version. Would you recommend completely moving over to 7.0.1 and avoiding 6.3 all together?

Thank you.

Saurabh

Hi Dr. Eastman,

I'm running the same structure with OpenMM 7.0.1 installed using conda on OSx 10.11 with CUDA 7.5 now. It'll take some time to run, and I'll let you know if it still runs into errors.

Thank you.

Saurabh

Hi, I'm running a protein in water box system with the AMOEBA force field on an iMac NVIDIA GPU on the CUDA platform using OpenMM6.3 compiled from source. My system is ~30k atoms including waters. I'm running an NVT simulation with the Langevin integrator. However, I'm noticing a stochastic error th...