AMBER Archive (2003)

Subject: Re: AMBER: variable not in namelist for Sander input

From: Thomas E. Cheatham, III (cheatham_at_chpc.utah.edu)
Date: Mon Jul 21 2003 - 13:18:50 CDT

> After deleting ntwxm, ntwem, the MD runs in Sander at AMBER6. However, it
> seems it started to change the octahedral box to a cubic box, because teh
...
> The input line for PME is "
> &ewald
> nfft1=90,nfft2=90,nfft3=80,order=5,dsum_tol=0.00005,
> &end

The output file from AMBER6 will tell you what kind of box it thinks it
has. From my test run on my system, I saw:

     BOX TYPE: TRUNCATED OCTAHEDRON

There are a number of ways this box information is detected (in AMBER6).
[In AMBER7, this information is primarilly contained in the input/restrt
coordinates.]

At the bottom (of the AMBER6 style) prmtop file is all the box
information. The first number is the "angle" and the rest of the numbers
are the x, y, and z. For a truncated octahedron, this should be
1.09471219E+02. [This is really a hack since ALL the angles are 109.47...
for a truncated octahedron not just one of the numbers.] In the inpcrd
files, six numbers are present, x, y, z, alpha, beta, gamma. Like:

  55.7544809 55.7544809 55.7544809 109.4712190 109.4712190 109.4712190

If the prmtop does not have 109.47.. then likely you didn't build the
truncated octahedron with the solvateOct command in LEaP (with the "iso"
keyword specified). If it does, perhaps you did a minimization which blew
away the box information in the restrt file (which no longer happens with
AMBER7). In this case, override the box information in the Ewald
namelist:

 &ewald
  nfft1=90,nfft2=90,nfft3=80,order=5,dsum_tol=0.00005,
  alpha=109.4712190, beta=109.4712190, gamma=109.4712190,
 &end

In this case you may want to update the box information if it changed from
previous MD (i.e. if you are doing MD + minimization cycles with
constant P).

Good luck,

\ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy
| Departments of Medicinal Chemistry and of University of Utah
| Pharmaceutics and Pharmaceutical Chemistry 30 South 2000 East, Room 201
| & Center for High Performance Computing Salt Lake City, Utah 84112
|
| e-mail: tec3_at_utah.edu phone: (801) 587-9652 FAX: (801) 585-9119
\ http://www.chpc.utah.edu/~cheatham Offices: BPRP295A / INSCC 418

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