From: Evandro Semighini (
Date: Tue May 19 2015 - 12:45:53 CDT

Hello Brian,

Thanks again !

1- I read it and saw the difference between the force fields that was
confusing me, but a friend of mine, that works with GROMACS and AMBER FF,
told me to try the chelp charges.

2 an 3- God point, got it.

4- I got the files generated from fftk, it takes at least 3 hours for every
run with one processor (with more, it crashes) in an Intel Core i3 2100

Unfortunatelly, the last advice will be the hardest part to get. =/

Thank you Brian !


2015-05-19 12:51 GMT-03:00 Bennion, Brian <>:

> Hello,
> Please read Dr. Mayne's paper that describes ffTK, it will provide insight
> on question 1 (ie how charges are determined for the charmm forcefield).
> Question 2. It is up to you to decide if the penalties given by
> are worth worrying about. If someone needed to
> repeat your work and they parameterized everything de novo, would you trust
> their results if they differed from your results?
> Question 3. If you don't optimize the bonded parameters then you get what
> the cgenff forcefield supplies (or doesn't supply for that matter). The
> forcefield has NO idea that your compound needs to be "frozen" in that
> docked conformation, unless you tell it by giving it the appropriate
> parameters. Please realize that the docked conformation represents a
> theoretical complex at 0 Kelvin. Will you or others do the experimental
> studies at 0 Kelvin?
> Question 4. It depends if you are running he calculation correctly or if
> your hardware/software is properly setup for these calculations.
> These questions point out that you need to do some more reading and ask
> for guidance from your mentor/supervisor.
> Sincerely
> Brian Bennion
> ------------------------------
> *From:* [] on behalf of
> Evandro Semighini []
> *Sent:* Tuesday, May 19, 2015 6:06 AM
> *To:*
> *Subject:* vmd-l: Questions regarding fftk and Gaussian
> 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