Re: [AMBER] Membrane protein tutorial

From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 10 Jun 2014 12:35:56 -0400

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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jun 10 2014 - 10:00:03 PDT
Custom Search