Re: Re: ffTK problem: initial parameter fiel is viod of atoms!

From: Zeinab Emami (
Date: Mon Oct 20 2014 - 11:33:25 CDT

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,*

On Mon, Oct 20, 2014 at 5:55 PM, Mayne, Christopher G <>

> 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:
> 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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