VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Mon May 21 2012 - 04:20:58 CDT

Hi
On last February I asked (VMD mailing list) how to use fftk for
transition metal enzymes. The developers kindly suggested what could
be tried, pointing out, however, that fftk was not designed for
TS-metal clusters. I did not succeed. I solved the task outside fftk,
as I did previously for related cases, along two lines, one by simply
using antechamber/gaff, with conversion to charmm ff through available
software, the other one through R.E.D., getting a mol2/ff file and
then manually arranging the frcmod file.

Now, as charmm should better suited for a simulation I am aimed at, I
am back to fftk for a small molecule comprising C,H,O,N,S atoms only.
Therefore, it should be suitable for fftk Two questions:

1) In which order the various components of fftk should be run? I only
have the PDB and a simple mol2 files, not comprising the FF.

2) At which level should QM calculations be carried out in view of the
presence of sulfur atoms?

Thanks for advice

francesco pietra