Hi Dr. Cheatum,
Thanks for the reply and suggestions.
My ligand is a disaccharide. According to GLYCAM naming conventions the
disaccharide has three residues, so my ligand is from residues 52-54.
I did the centering and imaging for 1-51 residues. The water box appears
weird.
I'm attaching the pdf of the box.
I'm running an NVT simulation. The attached pdf is the first snapshot of the
system.
I'm pasting my NVT md input file. Do you think that the simulation has some
intrinsic problems?
-----
&cntrl
imin = 0,
irest = 1,
ntx = 5,
ntb = 1,
cut = 10.0,
ntr = 0,
ntc = 2,
ntf = 2,
temp0 = 300.0,
ig = -1,
ntt = 3,
gamma_ln = 1.0,
nstlim = 5000000, dt = 0.002
ntpr = 10000, ntwx = 25000, ntwr = 25000
/
-------------
Sorry if these are to naive questions.
Regards
Sai
On Thu, Aug 25, 2011 at 5:06 PM, Thomas Cheatham III <tec3.utah.edu> wrote:
>
> > 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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Received on Wed Aug 31 2011 - 14:00:02 PDT
