On Fri, 2014-02-28 at 15:35 +0000, almarques wrote:
> Hi,
>
> Thank you. Indeed I am using ambertools12 but ambertools13 will be
> installed in the lab computers in the next few days. The error that you
> found is similar to the one reported in:
>
> http://archive.ambermd.org/201306/0453.html
>
> Since in my solvated topology file the Na+ ions are before the
> non-standard water molecule bound to Mn atom do you think that I will
> have to re-order the atoms (i.e, use fix_traj_parm.py)to assure
> compatibility between the trajectory without water and ions and the
> topology file of the complex without water and ions? Because, if I
> extract a pdb from the trajectory without solvent/ions the atoms are in
> the same order as the pdb file generated from the topology file without
> water/ions.
You should not use fix_traj_parm.py; it is incredibly slow [1] and
fixatomorder in cpptraj will do it far more quickly. (Dan had not
written fixatomorder when I wrote that script).
While you might not _have_ to use fixatomorder for MMPBSA.py to work for
your system, it will definitely not hurt. Once you have AmberTools 13
installed and updated, I suggest fixing the trajectories using
fixatomorder in cpptraj.
HTH,
Jason
[1] I believe I made a critical performance mistake with
fix_traj_parm.py in which coordinate access actually fetches individual
coordinates out of the file rather than storing a whole frame in memory
and accessing coordinates from there. I could probably make the script
orders of magnitude faster by fixing that problem, but there's no point
now that you can use fixatomorder in cpptraj.
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Feb 28 2014 - 08:30:02 PST
