VMD-L Mailing List

From: Evandro Semighini (epsemighini_at_gmail.com)
Date: Tue May 19 2015 - 08:06:47 CDT

Hello VMD community !

I'm new to NAMD and VMD and have some questions about the parameterization
of the molecules I got from virtual screening assays.

I got a huge help from the NAMD mailing list and it leaded me to another
kind of problems and doubts, regarding fftk and Gaussian, that I was unable
to solve by myself/searching, so, here I am.

I was instructed by mrs. Crystopher Mayne and Brian Bennion to use
ParamChem and then cut the molecules in pieces with molefracture to
optimize them with fftk and Gaussian, and there's where I am stuck now.

As my molecules are sort of big, fftk creates more than 90 water
interaction files to be loaded to Gaussian for each one, and I have more
than 30 molecules.
1- Do I really need to run all of this water optimization in Gaussian or I
can run just the geometry optimization, which calculates new charges ?
2- If no, can I run only the interactions for the highest penalized atoms
or, there is other method with lower time cost ?
3- Do I really need to optimize the angles and dihedrals penalties, as my
molecules are in the docked conformation ?
4- I never used quantum softwares before, so, is it normal this
calculations take several hours to end ?

Thank you in advance for any help.

Evandro Semighini