-
After preparing my files in gromacs(please let me know if there is any other way of doing this) I tried :
python openbpmd.py -s solv_ions.gro -p topol.top -o ligand0_pose0 -lig_resname MOL -nreps 5
…
-
Would someone please tell me if OpenMM can do something called Gaussian accelerated molecular dynamics? If yes, is this particularly difficult to set up/do? I am totally new to OpenMM so I'd like to…
-
I am following [ParmEd example with OpenMM and CHARMM](https://parmed.github.io/ParmEd/html/omm_charmm.html#generalized-born-implicit-solvent), but instead of using the supplied PSF file I am trying t…
-
Hi everyone,
In [my previous post](https://github.com/ParmEd/ParmEd/issues/933), I mentioned that I have to first convert a GROMACS format topology file to AMBER format, then back to GROMACS again.…
-
Hey, thank you so much for the great tool!
Is there any intention to update the CHARMM c36 to the newest parameters that were released on July 2021? I tried on my own to do this using the conversio…
-
Hello, I encountered an error while running the program, I have modified charmm.sh, why does the blade's runtime directory still point to/home/renaling?
/WorkflowForMSLD/MSLD_Simulations/run1_failed/…
-
Hello,
In the documentation for [CHARMM36](http://docs.openmm.org/latest/userguide/application/02_running_sims.html#charmm36) options, it suggests that the current CHARMM forcefield being run is th…
-
When I process the pdb file in CHARMM-GUI to apply amber19sb in GROMACS, I get a protein topology file and a force-field file.
Can I extract the atomtypes, bondtypes, pairtypes, angletypes, and dih…
-
what is the PDB file format in oddt(RSC PDB, charmm PDB)?
I want to calculate interactions (salt bridge, hydrogen bonds, etc ) between a protein and a short peptide which obtained from MD simulation…
-
Right now the charmm writer in mBuild isn't merged into the main branch. To avoid complications, @justinGilmer suggested we copy this code into the repository.