Hi, I really like that openmm is implemented in ChimeraX. Is it possible somehow to implement/include openmmforcefields (https://github.com/openmm/openmmforcefields)? Specifically, I often use custom residues and would love to, e.g. parametrise them using GAFF, to do some small local minimisation in ChimeraX. Or is there any way of passing force fields for ligands parametrised with GAFF to ChimeraX? Thanks, Józef
Hi Józef, ChimeraX includes the OpenMM package from PyPi. We don't try to build it ourself. I does not appear that OpenMM includes openmmforcefields and there is no PyPi package for openmmforcefields. If there were a PyPi package you could just use the ChimeraX command "pip install openmmforcefields" to install it into ChimeraX. In general we don't include packages in ChimeraX that are not used by the built-in tools. Tom
On Jan 24, 2025, at 12:31 AM, Lewandowski, Jozef via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi,
I really like that openmm is implemented in ChimeraX. Is it possible somehow to implement/include openmmforcefields (https://github.com/openmm/openmmforcefields)? Specifically, I often use custom residues and would love to, e.g. parametrise them using GAFF, to do some small local minimisation in ChimeraX. Or is there any way of passing force fields for ligands parametrised with GAFF to ChimeraX?
Thanks, Józef _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
As Tom says, we install OpenMM from PyPi, and there's no PyPi package for openmmforcefields. You might be able to add them "by hand" by taking the amber/charmm directories from the GitHub repository and dropping them into the openmm package's "data" directory in ChimeraX. You can find where openmm is installed with (in ChimeraX's Python shell): import openmm openmm.__file__ Also, if you run addcharge on your ligand then each atom's GAFF type will be in that atom's "gaff_type" attribute. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Jan 24, 2025, at 10:53 AM, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Józef,
ChimeraX includes the OpenMM package from PyPi. We don't try to build it ourself. I does not appear that OpenMM includes openmmforcefields and there is no PyPi package for openmmforcefields. If there were a PyPi package you could just use the ChimeraX command "pip install openmmforcefields" to install it into ChimeraX. In general we don't include packages in ChimeraX that are not used by the built-in tools.
Tom
On Jan 24, 2025, at 12:31 AM, Lewandowski, Jozef via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi,
I really like that openmm is implemented in ChimeraX. Is it possible somehow to implement/include openmmforcefields (https://github.com/openmm/openmmforcefields)? Specifically, I often use custom residues and would love to, e.g. parametrise them using GAFF, to do some small local minimisation in ChimeraX. Or is there any way of passing force fields for ligands parametrised with GAFF to ChimeraX?
Thanks, Józef _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
participants (3)
-
Eric Pettersen -
Lewandowski, Jozef -
Tom Goddard