Hi,
Your structure is in PDB format and contains no box coordinates, which
are necessary to perform imaging. If you can send along an Amber
restart file with box coordinates we can try to reproduce exactly the
imaging behavior you are seeing. That said, it looks like your solute
may be too big for the size of the box it is in, so getting it
completely surrounded by solvent may be difficult. You could try
experimenting with centering on different parts of the solute to see
if that makes it fit inside the box better; there needs to be enough
clearance on each side of the solute so that at least one water
molecule can fit between the solute and the box edge prior to imaging.
-Dan
On Thu, Oct 10, 2013 at 8:41 AM, Heribert Reis <hreis.eie.gr> wrote:
> Hi Jason,
>
> My colleague used the script as proposed by you, but the resulting
> structure was the same as the original one; the coordinates were unchanged.
>
> Then he tried this:
>
> center :1-581 origin
> image origin center familiar
>
> which shifted the protein into the unit cell, but still has close contacts,
> now inside the unit cell. What could be wrong here?
>
> I'm appending the original snapshot as a bzip2 file.
>
> Thanks,
> Heribert
>
>
> On Wed, Oct 9, 2013 at 6:22 PM, Heribert Reis <hreis.eie.gr> wrote:
>
>>
>>
>> ---------- Forwarded message ----------
>> From: Jason Swails <jason.swails.gmail.com>
>> Date: Wed, Oct 9, 2013 at 6:06 PM
>> Subject: Re: [AMBER] Shifting molecules by a box length
>> To: AMBER Mailing List <amber.ambermd.org>
>>
>>
>> On Wed, Oct 9, 2013 at 10:53 AM, Heribert Reis <hreis.eie.gr> wrote:
>>
>> > Hello,
>> >
>> > >From a colleague I got the cartesian coordinates of a snapshot from a
>> > AMBER-MD run of a protein molecule surrounded by water, which I would
>> like
>> > to use now in a different program. I just need the protein molecule,
>> fully
>> > surrounded by a layer of water. In the snapshot the protein molecule is
>> not
>> > fully inside the unit cell (sticking out in z-direction), so I need to
>> > shift some of the water molecules by one box length, but however I do
>> that,
>> > I end up with much too short distances between some of the shifted water
>> > molecules and atoms of the protein.
>> >
>> > The unit cell is a truncated octahedron, the triclinic cell length is
>> about
>> > 97 Ang (in all 3 directions), so according to some previous messages in
>> > this list, I multiply this by sqrt(3)/2 to get the cubic box length of
>> ~112
>> > Ang (which is also about the max distance between the water molecules in
>> > z-direction, so that seems to be about correct), but just adding this
>> > number to the z-coordinates of the waters I end up with those very short
>> > distances, so I guess that is not the correct procedure. What would be
>> the
>> > correct way to do it?
>> >
>>
>> You can use cpptraj to image the water into a periodic cell centered on
>> your solute. The following cpptraj script should do what you want it to
>> do:
>>
>> parm <your_prmtop>
>> trajin <your_trajectory>
>> autoimage
>> trajout <imaged_trajectory>
>>
>> <your_trajectory> can be any of a number of formats (NetCDF trajectory,
>> ASCII trajectory, PDB, etc.). <your_prmtop> can be an Amber topology
>> file or PDB file. The imaged_trajectory can be written as a PDB file
>> (.pdb), NetCDF trajectory (.nc) or normal ASCII trajectory file (.mdcrd)
>> based on the extension of the file name (or it can be explicitly set in the
>> trajout command).
>>
>> cpptraj is then run like:
>>
>> cpptraj -i <script_file>
>>
>> This is all detailed in the AmberTools manual.
>>
>> HTH,
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>
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>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Oct 10 2013 - 08:30:03 PDT
