VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Fri Jun 13 2008 - 07:34:42 CDT

On Thu, 12 Jun 2008, Nicolas wrote:

NS> Thanks,
NS>
NS> If pmepot just need the partial charges, generate a *.psf sounds the easiest

yep.

NS> solution. For the moment, I just have a *.top generated by GROMACS. But VMD
NS> should be able to create *.psf. So, I will just have to correct the charges
NS> with a couple of awk/sed commands...

if you save the preprocessed(!) .top file from gromacs (-pp flag
in grompp, IIRC), you may be able to generate a useful .psf with

http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/top2psf/

cheers,
   axel.

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

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.