Re: [AMBER] Membrane protein tutorial

From: Brian Radak <radak004.umn.edu>
Date: Tue, 10 Jun 2014 13:03:45 -0400

But doesn't sander/pmemd adjust ifbox on-the-fly based on the lattice
vectors in the restart file? I've seen this happen with triclinic boxes for
example. I suppose the important thing is that ifbox > 0, which usually
requires you to use solvateBox or solvateOct in tleap or else set box.



On Tue, Jun 10, 2014 at 12:35 PM, Jason Swails <jason.swails.gmail.com>
wrote:

> On Tue, Jun 10, 2014 at 12:19 PM, Brian Radak <radak004.umn.edu> wrote:
>
> > IFBOX is a (mostly) deprecated flag
> > in the prmtop.
> >
>
> ‚ÄčI disagree with this statement. IFBOX is a pointer that indicates whether
> a box is present or not as defined in the topology file. A value of 0
> means there is no box present. A value of 1 means the box is orthorhombic.
> A value of 2 indicates it is a general triclinic (typically a truncated
> octahedron if set by tleap). There are no plans to retire the use of this
> flag as far as I know, and it is frequently used in error checking as well
> as telling sander and pmemd what sections of the topology file should be
> present (e.g., ATOMS_PER_MOLECULE, SOLVENT_POINTERS, BOX_DIMENSIONS, etc.).
> See http://ambermd.org/formats.html
>
>
> If you are getting a complaint that IFBOX is 0 for a system you intend to
> treat with periodic boundaries, that typically means you loaded a PDB file
> that already had all solvent atoms present and didn't use the "setBox"
> command in tleap (or, alternatively, "set box {dimX, dimY, dimZ}"). Check
> the membrane tutorial again, since this command is present.
>
> All the best,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>



-- 
================================ Current Address =======================
 Brian Radak                                             :     BioMaPS
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Received on Tue Jun 10 2014 - 10:30:02 PDT
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