Hello,
I am running into an issue which I can't find documented anywhere. I can't import swm4ndp.xml water file to the Forcefield object, according to the documentation, when using the charmm drude 2019 force field.
Warning Drude polarizable sites and lone pairs are not yet supported by ParmEd and the CHARMM36 forcefields that depend on these features are not included in this port. To use the CHARMM 2019 polarizable force field[12], include the single file charmm_polar_2019.xml.
I do see that the swm4 water in the charmm_polar_2019.xml file so that I should be able to add it. According to the documentation for adding solvent via the modeller.addSolvent command, this model is not supported:
Allowed values for the model option are 'tip3p', 'tip3pfb', 'spce', 'tip4pew', 'tip4pfb', and 'tip5p'. Be sure to include the single quotes around the value.
So technically this is not an option. However, choosing the option model='tip5p' does "work" because swm4 is a 5-point water model. The resultant atom names in the pdb of the system and definitions of the swm4 water model in the .xml file seem different so it's unclear if I'm actually using the correct water model. I am wondering if:
- This is actually the correct method for doing this?
- And, if it is, could a note of this be made in the documentation so it is clearer how to accomplish this? Given the process for using this force field is already different from most of the nonpolarizable force fields, it feels unclear and I had to hope that the tip5p option would be interpretted correctly.
Thanks again!
Brian
Hello,
I am running into an issue which I can't find documented anywhere. I can't import swm4ndp.xml water file to the Forcefield object, according to the documentation, when using the charmm drude 2019 force field.
Warning Drude polarizable sites and lone pairs are not yet supported by ParmEd and the CHARMM36 forcefields that depend on these features are not included in this port. To use the CHARMM 2019 polarizable force field[12], include the single file charmm_polar_2019.xml.I do see that the swm4 water in the charmm_polar_2019.xml file so that I should be able to add it. According to the documentation for adding solvent via the modeller.addSolvent command, this model is not supported:
Allowed values for the model option are 'tip3p', 'tip3pfb', 'spce', 'tip4pew', 'tip4pfb', and 'tip5p'. Be sure to include the single quotes around the value.So technically this is not an option. However, choosing the option
model='tip5p'does "work" because swm4 is a 5-point water model. The resultant atom names in the pdb of the system and definitions of the swm4 water model in the .xml file seem different so it's unclear if I'm actually using the correct water model. I am wondering if:Thanks again!
Brian