Scoring a small molecule conformer using any of the tinker-hp available force fields? [question]

[UnixJunkie]

Hello,

Is there some example code demonstrating this:

• I have a small molecule in 3D
• I would like to know the internal energy of the molecule; e.g. using OPLSAA

Thanks!

[louislagardere]

Hi, You would need to get the parameter and topology files first, if it's a protein in the pdb format you can use the "pdbxyz" program of the tinker suite, otherwise you need to resort to an external program to get them (poltype for AMOEBA, charmm-gui for CGenFF and ligpargen for OPLS). You can look into this documentation https://github.com/louislagardere/winter-school-2023/blob/main/Tinker_Winter_School.pdf to get information about how to get energies then. Note that for small molecules in the gas phase I recommend the use of Tinker 8 as Tinker-HP is mainly designed to use periodic boundary conditions with PME.

[UnixJunkie]

Thanks a lot, especially for the gas phase tip (I am interested in a vacuum calculation).