Hi Jason,
I ended up using your suggested method. Thank you very much for the help.
-Joe
----- Original Message -----
From: "Jason Swails" <jason.swails.gmail.com>
To: "AMBER Mailing List" <amber.ambermd.org>
Sent: Friday, February 1, 2013 8:22:54 PM
Subject: Re: [AMBER] Problem using solvatebox for large, linear peptide
On Fri, Feb 1, 2013 at 6:32 PM, Joe Passman <joepassman.comcast.net> wrote:
> Thanks for the information. I am need of solvating the entire protein. I
> would like a big enough buffer region to prevent interactions among
> replicas. What do you suggest for an appropriated buffer size? The radius
> of gyration for my system is about 21 ang. I would like to be able to
> vizualize the information in vmd, so a fix before the move to mmCIF would
> be awesome .
>
Why not just visualize the prmtop and inpcrd file directly in VMD? Why do
you need to go through a PDB file? If you must have a PDB file, perhaps
try cpptraj, but there are no guarantees such a large system is supported
in PDB format from this source, either.
Maybe try the original 20A buffer and see what the box dimensions are --
they may be large enough to allow free rotation (and, like Dave suggested,
a truncated octahedron may be a much better choice for you).
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Feb 05 2013 - 13:00:02 PST
