From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Mon Oct 20 2014 - 11:45:39 CDT
Zeinab,
I should specify that in the screencast tutorials we did not include the standard CGenFF parameter file as the "associated parameter file" because we wanted to treat pyrrolidine as if it were completely unknown (it is included in the standard CGenFF files). When building the initialized parameter file, ffTK first determines all of the parameters needed to describe the molecule (using the information in the PSF), and then crosschecks these required parameters against any parameter sets listed as "associated parameter files." ffTK will only write out the parameters that it does not find. In this case, if you included the CGenFF parameter file, ffTK will find all of the parameters it is looking for and will generate an empty parameter file.
Let's move this over to VMD-L for future discussions.
Regards,
Christopher Mayne
On Oct 20, 2014, at 11:33 AM, Zeinab Emami wrote:
Dear Christopher Mayne,
Thank you for your email. You are right, I did not notice this. I will forward my email to VMD-list now. About including a CGenFF parameter file,
I have been far from it for recent few days, though as far as I remember I followed exactly all the steps in the videos. I will consider it when I go back to
calculation again.
Best Regards,
Zeinab
On Mon, Oct 20, 2014 at 5:55 PM, Mayne, Christopher G <cmayne2_at_illinois.edu<mailto:cmayne2_at_illinois.edu>> wrote:
Zeinab,
Since ffTK is a VMD plugin, you should be asking this question in VMD-L, not NAMD-L.
Did you include the CGenFF parameter file (or any other file) as an "Associated Parameter File"?
Chris
Hello,
I am trying to test production of parameter files following the molefacture
tutorial and these video series about ffTK:
http://www.ks.uiuc.edu/Research/vmd/minitutorials/fftk/
http://www.ks.uiuc.edu/Training/Tutorials/vmd-molefacture/tutorial-Molefacture.pdf
I loaded my molecule to VMD, then invoked molefacture, edited the atom
names, charges and type. then using "file/ write psf and pdb file" produced
the psf and pdb files I need for the ffTK procedure. [VIDEO 1]
Then, I loaded the psf and pdb file in fftk/BuildPar/Identify Missing
Parameters and produced the parameter file, as it is described in the video
2.
The proper parameter file, as shown in video 2, should contain the atoms
and the values for bonds, angles and so on; and the values are set to zero.
Although, in the parameter file I got, there is no value, just comments; it
seems to me that VMD cannot read the pdb and psf files produced by
molefacture.
I hope these info are enough.
Best Regards,
ZE
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