VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Thu Aug 20 2015 - 12:23:09 CDT

Francesco,

I responded here: http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/26205.html

MP2 is the level of theory prescribed by the CHARM General Force Field to accurately describe the internal dynamics of molecule. Further, it is generally accepted practice to take a "divide and conquer" approach to parameterize large ligands.

Regards,
Christopher Mayne

On Aug 20, 2015, at 10:13 AM, Francesco Pietra wrote:

Hello:

I posted recently about ffTK OPT MP2 problems, no answer, however it became clear that the shared memory on a node (120GB) was not enough, and could not be increased. On the other hand, Gaussian is threaded, so that I can't exploit the enormous resources of the cluster.

Therefore, my question is, is OPT at MP2 really needed for getting a good ff for ligands along ffTK in the realm of classical MD? OPT at SCF level, followed by single-point MP2 is not enough? I understand that it depends on what one is looking for, from simple docking to normal mode calculations, so that my question covers all situations.

If SCF followed by single-point MP2 is not enough, the only alternative that I can see is to break the ligand into pieces and carry out OPT/MP2 on each piece, allowing for the approximations in reforming the whole ligand.

Thanks a lot for advice on strategy.

francesco pietra