Date: Tue, 30 Aug 2011 15:07:49 -0400
Hello,
I have a similar problem. In my case, all the waters are put back into the periodic box but there seem to be ordered vacuum regions (see the picture). This is how the system looks like after 15 ns in an NPT ensemble. I do get an empty token warning:
PTRAJ: center :1-201 mass origin
Mask [:1-201] represents 2940 atoms
PTRAJ: image origin center familiar
Warning: empty token?
Mask [*] represents 25672 atoms
Just reading the manual and some previous posts in this subject, I had the impression that I don’t really have to define a token using image. What's it that I'm missing?
Thanks!
Aysegul
________________________________________
From: Thomas Cheatham III [tec3.utah.edu]
Sent: Thursday, August 25, 2011 6:06 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Ptraj and wrapping water molecules
> I have a system with a protein bound by a ligand non-covalently.
> After running the NVT simulation for 10ns, I was trying to image the system
> to wrap the water molecules, but I could not.
> The sets of commands I used
>
> I. center :1-54 mass origin
> image origin center
OK, that centers residues 1-54 to the origin, and images around the
origin using the center of mass of each molecule. All molecules center of
masses WILL be inside the periodic box unless there is some error in the
imaging which is unlikely.
> II. center :1-54 mass origin
> image origin center triclinic
The same, except that the triclinic box shape will be observed.
> III. center mass origin
> image origin center
This centers either nothing or everything, followed by imaging.
> I was reading earlier posts by various members of the community but still
> could not solve the issue. The issue is, not all the water molecules are
> wrapped back into the box. Some water molecules still appear outside the
> box.
All of these methods should put all of the waters into the periodic box.
Whether solute is in the box will depend on the centering, i.e. parts of
it may appear outside the box (with a hole in the water on the other side
where the solute outside the box periodically should be).
If residues 1:54 include the ligand, do instead
center :1-53 mass origin
image origin center
However, regardless, are you sure waters are outside the box? If you
happened to not have run constant pressure you could have vacuum bubbles
(which might make it look like molecules are outside the box). Some
visualization programs can display the periodic box boundaries or you can
create a PDB file that puts "atoms" at the box vertices and use CONECT
records to draw the box lines.
--tec3
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