Molcas Forum

vkj

Member

Registered: 2019-04-10

Posts: 29

QM/MM setup with tinker

Dear developers,

is there a manual which details how to setup tinker.key for qmmm system setup with tinker ? I have tried to scour the molcas manual and there are only scant examples in espf section which are not very clear as to the description of various keywords. If I'm not wrong the tinker.key keywords used there are also not documented in tinker manual.

I am interested in quite a simple QM-solute + tip3p solvent setup, where I will optimise the QM solute in completely fixed tip3p waters taking into account the VDW + Electrostatics between solute and waters. This is inline with the averaged solvent optimization of Olivucci et al. (https://pubs.acs.org/doi/10.1021/acs.jctc.7b00860)

niko

Member

From: Marseille

Registered: 2015-11-08

Posts: 59

Website

Re: QM/MM setup with tinker

Hi,

There is no doc regarding QM/MM in the official Tinker distribution since Molcas is using a modified version of 6.3.3.

What is not clear in https://molcas.gitlab.io/OpenMolcas/sph … /espf.html? Could you be more specific? Facts are much appreciated.

After having installed the patched version of Tinker6.3.3 using the patch2tinker utility in the Tools directory, you need to specify in Tinker's key file the number of atoms you want Molcas to know about (QMMM keyword) and then specify the MM or QM nature for each of them. Regarding your case, you probably don't need any link atom. By the way, after having finished the Tinker setup (xyz and key files), you can use Tinker's xyzedit utility to create automatically a molcas template input.

Hope this helps

vkj

Member

Registered: 2019-04-10

Posts: 29

Re: QM/MM setup with tinker

The keywords  used in  QMMM.key in the espf example section  are not very clear to me , if they are describing number of atoms or atoms index etc. Also in the QM keyword there is a negative number which makes it even more mysterious.

niko

Member

From: Marseille

Registered: 2015-11-08

Posts: 59

Website

Re: QM/MM setup with tinker

OK, the QMMM keyword is followed by the number of atoms which are known by Molcas.
Then comes the index of each of these atoms, starting with either QM, MM or LA, respectively for QM, MM or link atoms. The convention for this notation is Tinker's one (see https://dasher.wustl.edu/tinker/). For instance, -X Y means all atoms comprised between X and Y (both included). Accordingly, "QM -8 10 7 12 13" means atoms 8, 9, 10, 12 and 13 are QM atoms.

I really encourage you reading Tinker's manual and run a couple of Tinker only calculations first.