AMBER Archive (2008)

Subject: Re: AMBER: not equivalent oxygens in COO- / how to force order of atoms in IMPROPER?

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Wed Mar 19 2008 - 12:26:24 CDT

Hi Edyta:
Please, put me in the list of those very much interested in your Python script.
Sincerely

francesco pietra

--- Edyta Malolepsza <em427_at_cam.ac.uk> wrote:

> Dear David,
>
> > > The reason can be in order of atoms in IMPROPER angles for NH2 and COO-
> groups.
> >
> > This will only really be fixed by a change in the way the impropers are
> > defined, I think. Someone will have to take this on as a project; it will
> > be easier once we implement the CHARMM force field equations (but don't
> hold
> > your breath.)
>
> It can be done also by reordering atom positions in topology file
> without any code or energy formula change. I have written program in
> python which reads original topology file and AMBER libraries for
> amino acids and nucleic to create new topology file with correct order
> of atoms for IMPROPER's. With new topology file any permutations of
> equivalent atoms give the same results - potential is symmetric.
>
> I can share this program, please let me know if somebody is interested.
>
> With best regards,
>
> Edyta Malolepsza
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>

      ____________________________________________________________________________________
Looking for last minute shopping deals?
Find them fast with Yahoo! Search. http://tools.search.yahoo.com/newsearch/category.php?category=shopping
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu