From mls%!at!%wucmd.wustl.edu  Fri Sep 18 04:42:55 1992
Date: Fri, 18 Sep 92 09:42:55 -0500
From: mls.,at,.wucmd.wustl.edu (Mark Smythe)
To: chemistry: at :ccl.net
Subject: non-aqueous solvation : summary



Dear netters,

In response to my query on non-aqueous solvation using Amber Charles Foley
writes.



  Some types of non-aqueous simulations can be done with the AMBER code as is.
 I have run some periodic boundary simulations of a peptide in methanol.  The
 steps involved are:  1) add the methanol parameters to the database.  I used
 the parameters from Jorgensen:  J. Phys. Chem. 94, 1683 (1990)
                                J. Phys. Chem. 90, 1276 (1986).

 2) Create a PDB file with your solute surrounded by the appropriate box of
 solvent molecules.

 3) Create a prep file for you solvent molecule.

 4) Create a link.input file defining the solute and surrounding solvent
    molecules.  Define each solvent molecule as a separate molecule in link.

 5) Create an edit.input file that creates a "dummy" box.  This means you use
   the "BOX" option to add waters, but set the closeness of approach
    parameters so that no waters will actually be added.  You should also use
    the "XRAY" option to read in the PDB file you created above.

 6) Create a parm file for the system.  Now edit the resulting topology file.
    Do the following:

        A) Search the file for a line starting with either "0.90000000E+02"
           or " .90000000E+02" (depending on whether your system writes the
          leading 0).  This line contains the dimensions of the box.  You
           will need to know these, and replace them in this file.  The
           values on this line are:

           angle        boxx    boxy    boxz

           Change only the box dimensions to reflect the size of the box in
           your PDB file.

        B) Search *backwards* in the file, starting with the second line above
           the line you modified in (A), for the first line that contains
           three, and only three, values.

           The values on this line are

           IPTRES       NSPM    NSPSOL

           IPTRES: Set to the number of the last *residue* to be considered
                   part of the solute.

           NSPM: Do not modify

           NSPSOL: Set to the number of the first *molecule* to be considered
                   part of the solvent.
7) If you are running with SANDER/MINMD, you're done.
   If you are running with GIBBS, you should set the variable ITIP in the
   input to 1, to indicate you are using a non-water solvent.



That should get you there.  I created my starting PDB file using a beta
release of LEAP, the graphical AMBER interface.  You might be able to get a
copy of this through UCSF.  The recipe for creating the box in AMBER was
done with great help from David Pearlman of Vertex Pharmaceuticals.  He is
one of the principle authors of AMBER 3.0A and is inimately familiar with
the details of the code.

You might consider directing any further queries regarding AMBER to the
mailing list maintained at UCSF.  To subscribe to the list, just send mail
> to amber-request _-at-_)cgl.ucsf.edu.  To send queries, comments, whatever, just
> send mail to amber $#at#$ cgl.ucsf.edu.  I have had good responses from people who
> read that list.

> Good Luck!


Charles K. Foley, Ph.D.
Cray Research, Inc.
Americas & Asia/Pacific Group
P.O. Box 12746
Research Triangle Park, NC 27709                                o
                                                              <(
ckf#* at *#f16.cray.com                                               [\.



In response to :
  ...  What types (MeOH, DMSO, etc) of different
 solvent boxes are available that have been suitably parameterised and
 tested?



 Sorry, not an Amber user (yet). But for GROMOS, there should be MeOH, CCl4
 (but there's a paper, telling full MD in CCl4 is not much better than SD
 with appropriate parameters) and DMSO (Rao+Singh: JACS _112_, 3803-3811
 (1990); Mierke+Kessler: JACS _113_, 9466-9470 (1991) + one more recently,
 I think). I seem to recall some rumours about CHCl3, but I might be veeery
 wrong ...
                Wolfgang.
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Thankyou to those who responded

Mark

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