From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Feb 16 2014 - 12:10:01 CST
On Sun, Feb 16, 2014 at 1:00 PM, zeynab mohamad hoseyni
<zmhoseyni_at_yahoo.com> wrote:
> Dear All,
>
> I followed NAMD membrane tutorial to align my protein with the membrane and
> producing two temporary files for
> each of membrane and protein. Then I tried to combine the produced
> temporary files into one set of psf and pdb files
> using the following commands as it is written in the tutorial:
> % mol delete all
> % package require psfgen
> 1.6
> % resetpsf
> psfgen) clearing structure, preserving topology and aliases
> % readpsf membrane.psf
> psfgen) reading structure from psf file membrane.psf
> psfgen) psf file does not contain cross-terms
>
> I don't understand what is the meaning of the message "psf file does not
> contain cross-terms". I used CHARMM36 to produce
> the lipid bilayer and I expect it contains the cross terms as well. Could
> any body help to understand what is wrong?
what makes you think that lipids should have cross-terms?
axel.
>
> Thanks,
> Zeynab
>
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 College of Science & Technology, Temple University, Philadelphia PA, USA International Centre for Theoretical Physics, Trieste. Italy.
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