AMBER Archive (2006)

Subject: AMBER: Problem with setbox command...

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Thu Mar 30 2006 - 01:44:37 CST

Dear All,

I have created a structure using nucgen (test.pdb). Then I used the
following script (xleap_01.in) in xleap to create the prmtop and inpcrd
files:

---------------------- xleap_01.in --------------------------
molecule = loadpdb test.pdb
solvateoct molecule TIP3PBOX 8.0
savepdb molecule test_xleap.pdb
saveamberparm molecule prmtop_01 inpcrd_01
quit
-------------------------------------------------------------

Then, I have used the following script on the solvated structure created
in the above script (test_xleap.pdb).

---------------------- xleap_02.in --------------------------
source leaprc.rna.ff99
molecule = loadpdb test_xleap.pdb
setbox molecule centers
saveamberparm molecule prmtop_02 inpcrd_02
-------------------------------------------------------------

In this second case I am using the setbox command to create the box
information in the prmtop_02 file.

I ran these two prmtop/inpcrd files (for 5 ns). The first one
(prmtop_01/inpcrd_01) gave a reasonable structure at the end of the
simulation. But the second case gave a really weird structure at the end.
The water molecules are accumulated around 3-4 layers in the box, which
is of course not expected.

DAC wrote in one of his email that the usage of 'setbox' command is
tricky, and that I am using it wrong. But I do not know how I can create
the box info in the prmtop file without using the 'setbox' command.

Let me gave some more info about the inpcrd files. The last line in the
inpcrd files are as follows:

==> inpcrd_01 <==
  38.6491104 38.6491104 38.6491104 109.4712190 109.4712190 109.4712190

==> inpcrd_02 <==
  37.6940000 43.3120000 42.7090000 90.0000000 90.0000000 90.0000000

When I check out the prmtop files, too, these box info.s are given right:

==> prmtop_01 <==
...
%FLAG BOX_DIMENSIONS
%FORMAT(5E16.8)
  1.09471219E+02 3.86491104E+01 3.86491104E+01 3.86491104E+01
%FLAG RADII
%FORMAT(5E16.8)

==> prmtop_02 <==
...
%FLAG BOX_DIMENSIONS
%FORMAT(5E16.8)
  9.00000000E+01 3.76940000E+01 4.33120000E+01 4.27090000E+01
%FLAG RADII
%FORMAT(5E16.8)

I will really appreciate if you can give me some suggestions on how to
create the box info on, so that the md run wont give weird structures at
the end.

------------------------------------
PS: I was thinking to copy/paste the box info of the first inpcrd_01

  38.6491104 38.6491104 38.6491104 109.4712190 109.4712190 109.4712190

to the second inpcrd_02. Also I was thinking to change the box info in
the prmtop_02 file with the prmtop_01 box info.

  9.00000000E+01 3.76940000E+01 4.33120000E+01 4.27090000E+01

Is this reasonable to do?
------------------------------------ 

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
  - University of Rochester      -				-
  - Hutchison Hall, # B10        -				-
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  - http://www.pas.rochester.edu/~yildirim/			-
  ---------------------------------------------------------------

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