Amber masthead
Filler image AmberTools21 Amber20 Manuals Tutorials Force Fields Contacts History
Filler image

Useful links:

Amber Home
Download Amber
Installation
Amber Citations
GPU Support
Updates
Mailing Lists
For Educators
File Formats
7 Free Energies
 

(Note: These tutorials are meant to provide illustrative examples of how to use the AMBER software suite to carry out simulations that can be run on a simple workstation in a reasonable period of time. They do not necessarily provide the optimal choice of parameters or methods for the particular application area.)
Copyright Andrew T. Fenley & Michael K. Gilson 2014


Section 1: Building the topology and input coordinates files

This section describes the steps required to prepare the topology files for each of the simulations using the provided MOL2 and PDB files. In next section, we will generate the necessary input files for the various stages of simulation (minimization, equilibration, and production).

  1. Download the PDB or MOL2 files for each of the four simulations. Unless otherwise specified, we are using AM1-BCC charges and GAFF parameters. (Note, the MOL2 files for B2 and CB7 are needed for the simulation with B2 bound to CB7.)

    Simulation MOL2 PDB
    Pure Water --- water.pdb
    B2 b2_am1-bcc.mol2 ---
    CB7 cb7_am1-bcc.mol2 ---
    CB7 and B2 --- cb7_b2.pdb

  2. Make sure there are no missing parameters for either B2 or CB7 by running parmchk2 on the MOL2 files.

  3. Next, prepare the topology files (prmtop) and input coordinate (rst7) files for all of the simulations using tleap. The following leap scripts will generate the necessary topology and coordinate files and have been tested with tleap from AmberTools 14. Note, it is critical that the number of waters properly balance between the simulations representing the bound and unbound states. For this tutorial we are manually setting the water count to 1500 for each simulation.

    Pure water: water_tleap.in
    source leaprc.ff12SB
    # Load the PDBs
    structure = loadpdb water.pdb

    # Add water
    solvatebox structure TIP3PBOX 16.50 iso

    # Remove excess waters such that the total count is 1500
    remove structure structure.1509
    remove structure structure.1508
    remove structure structure.1507
    remove structure structure.1506
    remove structure structure.1505
    remove structure structure.1504
    remove structure structure.1503
    remove structure structure.1502
    remove structure structure.1501

    # Save topology files
    saveamberparm structure water.prmtop water.rst7

    # Quit
    quit

    The command

    tleap -f water_tleap.in

    will generate the following files: water.prmtop and water.rst7.

    B2: b2_tleap.in
    source leaprc.gaff
    source leaprc.ff12SB

    # Load any extra parameters
    loadamberparams b2_am1-bcc.frcmod

    # Load structure file MOL2
    guest = loadmol2 b2_am1-bcc.mol2

    # Add water
    solvatebox guest TIP3PBOX 13.16 iso

    # Remove excess waters such that the total count is 1500
    remove guest guest.1505
    remove guest guest.1504
    remove guest guest.1503
    remove guest guest.1502
    remove guest guest.1501

    # Save topology files
    saveamberparm guest b2.prmtop b2.rst7

    # Quit
    quit

    The command

    tleap -f b2_tleap.in

    will generate the following files: b2.prmtop and b2.rst7.

    CB7: cb7_tleap.in
    source leaprc.gaff
    source leaprc.ff12SB

    # Load any extra parameters
    loadamberparams cb7_am1-bcc.frcmod

    # Load structure file MOL2
    host = loadmol2 cb7_am1-bcc.mol2

    # Add water
    solvatebox host TIP3PBOX 10.18 iso

    # Remove excess waters such that the total count is 1500
    remove host host.1510
    remove host host.1509
    remove host host.1508
    remove host host.1507
    remove host host.1506
    remove host host.1505
    remove host host.1504
    remove host host.1503
    remove host host.1502
    remove host host.1501

    # Save topology files
    saveamberparm host cb7.prmtop cb7.rst7

    # Quit
    quit

    The command

    tleap -f cb7_tleap.in

    will generate the following files: cb7.prmtop and cb7.rst7.

    CB7 and B2: water_tleap.in
    source leaprc.gaff
    source leaprc.ff12SB

    # Load any extra parameters
    loadamberparams b2_am1-bcc.frcmod
    loadamberparams cb7_am1-bcc.frcmod

    # Load structure files MOL2 and PDB
    CUC = loadmol2 cb7_am1-bcc.mol2
    B2 = loadmol2 b2_am1-bcc.mol2
    b2host = loadpdb cb7_b2.pdb

    # Add water
    solvatebox b2host TIP3PBOX 9.91 iso

    # Remove excess waters such that the total count is 1500
    remove b2host b2host.1502
    remove b2host b2host.1501

    # Save topology files
    saveamberparm b2host cb7_b2.prmtop cb7_b2.rst7

    # Quit
    quit

    The command

    tleap -f cb7_b2_tleap.in

    will generate the following files: cb7_b2.prmtop and cb7_b2.rst7.

  4. We will now modify the box edges for each input coordinate file (rst7) such that each edge is exactly the same length (perfect cube). Later on, once equilibration is complete, we will modify the box lengths again to best represent a system at a constant 1 bar during an NVT simulation. Having the box edges identical in value at the beginning will make that later step easier.

    The last line of each input coordinate file (rst7) should look similar to the following (tail -n 1 *.rst7):

    Box Edges
    ==> b2.rst7 <==
    39.8061410 39.7571770 39.7967250 90.0000000 90.0000000 90.0000000

    ==> cb7.rst7 <==
    40.1760410 40.3426600 40.1360530 90.0000000 90.0000000 90.0000000

    ==> cb7_b2.rst7 <==
    40.1760410 40.3426600 40.1360530 90.0000000 90.0000000 90.0000000

    ==> water.rst7 <==
    39.5462090 39.7571770 39.5609130 90.0000000 90.0000000 90.0000000

    The first three numbers are the x, y, z box edge lengths. The remaining three numbers (all 90.0000000) are all box angles. Manually edit the rst7 files (e.g. using vim) such that the last lines match what you see below. Save the modified files as *_iso.rst7 (e.g. b2_iso.rst7)

    Modified Box Edges
    ==> b2_iso.rst7 <==
    39.8061410 39.8061410 39.8061410 90.0000000 90.0000000 90.0000000

    ==> cb7_iso.rst7 <==
    40.3426600 40.3426600 40.3426600 90.0000000 90.0000000 90.0000000

    ==> cb7_b2_iso.rst7 <==
    40.3426600 40.3426600 40.3426600 90.0000000 90.0000000 90.0000000

    ==> water_iso.rst7 <==
    39.7571770 39.7571770 39.7571770 90.0000000 90.0000000 90.0000000

    You may also download the prmtop along with modified rst7 files ready for simulation:

    Simulation Topology Input Coordinates
    Pure Water water.prmtop water_iso.rst7
    B2 b2.prmtop b2_iso.rst7
    CB7 cb7.prmtop cb7_iso.rst7
    CB7 and B2 cb7_b2.prmtop cb7_b2_iso.rst7

At this point, we have all the topology and structure files we need for the simulations. Now is a good time to visualize the structure files and make sure that everything appears correct.


Click here to go to section 2


Click here to go back to the Introduction


(Note: These tutorials are meant to provide illustrative examples of how to use the AMBER software suite to carry out simulations that can be run on a simple workstation in a reasonable period of time. They do not necessarily provide the optimal choice of parameters or methods for the particular application area.)
Copyright Andrew T. Fenley & Michael K. Gilson 2014