VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sat Jan 01 2011 - 16:09:04 CST

On Sat, Jan 1, 2011 at 4:12 PM, Jun Zhao <jz40_at_zips.uakron.edu> wrote:
> Dear Sir/Madam,
>
> I have simulated several protein systems using CHARMM MD (with psf).
> And I want to get IR spetra from MD trajectory.
> However, when I try to calclate amide I band data selecting "backbone and
> name NH",
> it said "insufficent charges to form a dipoe". I have already the psf data
> with charges data.
> What can I do?

the code you are using will compute the spectral density from
the total dipole moment of the selection, since IR adsorption
results from coupling of radiation to the dipole of your system.
with your selection you specify only one atom type, hence the
calculation fails (as the error message clearly tells you).

you have to expand your selection to include more atoms.

you cannot select a single band by picking specific atoms.

axel.

> --
> Jun Zhao
> PhD 2009 Chemical Engineering
> Room 301, Whitby House
> University of Akron
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.