VMD-L Mailing List

From: Nicolas (nsapay_at_ucalgary.ca)
Date: Thu Jun 12 2008 - 23:08:24 CDT

Thanks,

If pmepot just need the partial charges, generate a *.psf sounds the
easiest solution. For the moment, I just have a *.top generated by
GROMACS. But VMD should be able to create *.psf. So, I will just have to
correct the charges with a couple of awk/sed commands...

Cheers

Nicolas

Axel Kohlmeyer a écrit :
> On Thu, 12 Jun 2008, Nicolas Sapay wrote:
>
> NS> Hello,
>
> nicolas,
>
> NS> I want to use PMEpot on a trajectory computed using the OPLS-AA force field
> NS> (so charges different from CHARMM). I saw on the graphical it is possible to
> NS> load a name/charge map from a *.dat file. Where can I find the
> NS> specifications of this format? And is it possible to load this file from the
>
> check out.
> http://www.ks.uiuc.edu/Research/vmd/plugins/irspecgui/
>
> the format is rather simple and probably not flexible enough
> for what you need. if you have a proper topology file that
> VMD can read, it will contain the partial charges and you
> don't need to load those explicitly. the three options in
> the utility menu are basically "hacks". worst case, you can
> write a small script to read in whatever you want and assign
> it to the charge field of you atoms.
>
>
> NS> pmepot command line? (I don't see the option on the pmepot doc page) A last
> NS> question: I want do average the potential over the trajectory... Will pmepot
> NS> calculate the average potential directly or should I run it on every frame?
>
> see the Avg Frames field. syntax is the same as in the trajectory tab
> for graphical representations.
>
> cheers,
> axel.
>
> NS>
> NS> Thanks for your help
> NS>
> NS> Nicolas
> NS>
> NS>
>
>