AMBER Archive (2006)

Subject: RE: AMBER: Periodic boundary condition (PBC) > Problem now with ptraj

From: Rahaman, Asif (asif-rahaman_at_uiowa.edu)
Date: Thu Aug 31 2006 - 17:29:25 CDT

Dear Professor Cheatham,
 
I have a crystal of calcium carbonate. I have made residues for Ca(+2) and CO3(-2) and used water molecule (POL3). I have tried as you have suggested with the following scripts
 
ptraj.in
-----------------------------------------
trajin md.crd 1 5000 1
trajout traj.crd
box alpha 90.0 beta 90.0 gamma 74.8 fixalpha fixbeta fixgamma
center :1-544 mass origin
image origin center triclinic
-----------------------------------------------
 
I have deleted ' center @CA mass origin ' and added 'center :1-544 mass origin' as I have a total of 544 residues. Is that OK?
What do you think - any suggestions? The problem still exists.
 
Thank you very much again for your kind reply.
With best regards, Asif
 
P. S. If AMBER saves the last output coordinates and wrap it in the final .rst file, then ptraj should give the same results (structure) for the last step of trajectory - am I right??? Does AMBER and PTRAJ use different algorithm for wrapping molecules in the periodic box???????
 

________________________________

From: Thomas Cheatham [mailto:tec3_at_utah.edu]
Sent: Thu 8/31/2006 4:50 PM
To: Rahaman, Asif; amber_at_scripps.edu
Subject: RE: AMBER: Periodic boundary condition (PBC) > Problem now with ptraj

...assuming it is a protein, do:

  box alpha 90.0 beta 90.0 gamma 74.8 fixalpha fixbeta fixgamma
  center @CA mass origin
  image origin center triclinic

My guess is that your molecule has simply shifted such that it is no
longer in the center (i.e. spans across the periodic boundary).

> different from the structure obtained from the .rst file. The structure
> from the .rst file looks reasonable; but the one at the end of ptraj is
> wired. (it messes up - waters come in side the crystal where as the
> structure obtained from .rst file with IWRAP = 1 option water
> stays either on top or bottom of the crystal - which is reasonable - I
> think).

I think it is a matter of perspective; both are probably correct, just
each has the solute in a different place (and hence the waters in
different places)... Try the above and see if that resolves your issues.

--tom

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