VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Mon Jul 08 2013 - 15:00:28 CDT

ffTK is designed such that it will generate reasonable Gaussian input files for the user, but that those files are modifiable as advanced users see fit. You are free to modify the Z-matrix used to position the water molecule, as well as the degrees of freedom optimized by Gaussian. I will, however, caution you to make sure that you understand have ffTK parses and uses the resulting log files before modifying the input files by hand. During the charge optimization, ffTK will extract the optimized coordinates of the water water molecule from the Gaussian log file, and scan positions surrounding these optimized coordinates along a vector connecting the oxygen of the water to the interaction site (atom) specified in the QM Target Input. Modifying the Gaussian input to change the water position will change this interaction vector, so do so at your own risk. Also, take note that CHARMM generally tends to over polarize charges by scaling water interaction energies for neutral molecules by ~1.16 (an empirical scaling factor that can be modified directly in the Advanced Settings section).

Regards,
Christopher Mayne

On Jul 2, 2013, at 11:08 AM, surya narayanan chandrasekaran wrote:

Hi,

while Using FFTK in the charge optimization step the TK places three water molecules for a single carbonyl oxygen atom. and the interaction energy for the three positions are 120, 0.1, 120 Kcal/mol but the interaction energies are still higher and contradictory to literature values. so I reduced the angles and the IE reduces . so i wanted to know that whether repositioning of water molecule for interaction enrgies is acceptable or reliable.

Thank q
surya
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Suryanarayanan C
M.S Chemist
01742857830