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 -A_T- 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. +======================================+=====================================+ | Wolfgang Sauer | | | Institut fuer Organische Chemie I | "You have to be three standard | | Henkestr. 42, D-8520 Erlangen, FRG | deviations away from a normal | | | personality to like UNIX." | | sauer {*at*} organik.uni-erlangen.de | | | Tel.: 49/0 - 9131 - 85 - 2952 | Morris Jones (C&T) | | Fax: - 9132 | | +======================================+=====================================+ Thankyou to those who responded Mark ----------------------------------------------------------------------------- | Mark Smythe | Phone : (314) 935 4683 | | Center for Molecular Design | Fax : (314) 935 4979 | | Washington University | E-Mail: mls _-at-_)wucmd.wustl.edu | | Lopata Hall, Box 1099, One Brookings | | | Drive, St Louis, Mo, 63130 | | -----------------------------------------------------------------------------