From: ABEL Stephane 175950 (
Date: Fri Jul 24 2015 - 08:31:54 CDT

Hello everyone,

I am a new user of the fftk program and sorry if my question are naive I would like to improve the partial charges and the bonded parameters of a molecule that contains 49 atoms (pdb attached [1]). My molecule is formed with a polyOH benzene ring attached to a isopreneoid tail (i.e. (CHCH3CH2)2OH). My aim is to model this molecule by using the CGenFF force field. So I have firstly used Paramchem to see if the molecule is fully supported (i.e. w/o changes of the default parameters . Paramchem indicates higher penalties for some bonded parameters and atomic charges (49 and 22, respectively, see the results attached [2]). In particular some dihedrals have a penalty values around 22 and others around 4. So I am following the video tutorials and apply the fftk different steps to my molecule. Below my questions

1) Since the molecule has formed with 2 groups it is possible to use a "divide and conquer" approach (i.e. separate the molecule into two blocks) to speedup the optimization process? If yes how to choose the two molecular blocks (are there some rules we have to follow?)

2) In general it is safe to keep some parameters unchanged during the optimization process (those with penalty values ~ 0?

3) In the 3rd step (Water Int) I have selected only as donnors and acceptors the Hs and Os, respectively, However if I click on AutoDetct indice button fftk also includes in the list the C atoms as both donnors and acceptors (green sphere). I am confused about this selection since in the video tutorial the C atoms are not include in the charge derivations.



Thanks and sorry again if my questions are naive.


Stéphane Abel, Ph.D.

CEA Saclay DSV/IbItec-S/SB2SM & CNRS UMR 9198
Institut de Biologie Intégrative de la Cellule (I2BC)
Bat 528, Office 138C
Gif-sur-Yvette, F-91191 FRANCE
Phone (portable) : +33 6 49 37 70 60