Running a Go model with the AMHGMIN

GMIN can run various types of Go models with the AMH framework. This is useful for creating starting points for OPTIM, and also there are different forms of Go-like potentials that maybe interesting. To use this, first update and compile AMHGMIN as described in the GMIN Makefile.

Flags needed for GMIN input

The parameters behind the basin-hopping can be defined in the data file using the terms:

To begin with the AMH need to be turned on:

AMH

The interval of structures which are to be written to the file movie is termined by:

NINT_AMH    5

For structure prediction runs look something like this:

SLOPPYCONV  1.0D-3
TIGHTCONV   1.0D-3
UPDATES     5000
AMH
NINT_AMH    5
STEP  1.0 
MAXBFGS   1.0
TEMPERATURE 10.0

For slowly finding the lowest energy structure which is necessary as starting points for PATHSAMPLE runs shorter length steps, and much lower temperatures are necessary. The file then looks something like this:

SLOPPYCONV  1.0D-5
TIGHTCONV   1.0D-5
UPDATES     5000
AMH
NINT_AMH    5
STEP  0.4 
MAXBFGS   0.4
TEMPERATURE 1.0

Input files for AMHGMIN

There are several files that are necessary. Making sure the paths are correct is important. For running a Go model with AMHGMIN.

1. The primary input file is creatively called input_amh.

2. An alignment file which correlates the target sequence to the memory structures. In the most simple case there is one memory structure which is an experimental structure, but it does not need be. The following directory needs to be in the running directory. The directory in match/<filename>/filename.

3. The memory structure which defines the Go contacts is necessary. The following directory needs to be in the running directory. The directory in proteins/filename.

4. The strength of these interactions is defined by gamma.dat roughly speaking the interaction energy should be equally divided between local, medium, and long sequence separations.

5. A directory of input parameters which add certain parameters for the backbone interactions. The directory to copy is /home/mp466/amh/params into the running directory params.

CHARMM keywords

The toppar parameters that should be used are the EEF1.1.inp files. This is done using:

open read unit 11 card name toph19_eef1.1.inp
read rtf card unit 11
close unit 11

open read unit 12 card name param19_eef1.1.inp
read para card unit 12
close unit 12

The charmm keywords are as follows:

eef1 setup membrane slvt water slv2 chex nsmth 10 width 26.0 temp 298.15 -
unit 93 name "/home/jwll2/svn/CHARMM31/toppar/solvpar.1.inp" aemp 0.85
!gouy anfr 0.3 area 70. conc 0.1 offset 3.0 valence 1
update ctonnb 7. ctofnb 9. cutnb 15. group rdie

membrane introduces the membrane model and slvt water and slv2 chex specify that the exterior solvent is water and that the interior solvent is cyclohexane. nsmith, set to 10 as a default, determines how steep the transition is at the interface between interior and exterior. The width of the membrane can be altered by altering the value 26.0. This refers to the width of the membrane in angstroms and usually has a value 25-30. The last keyword aemp, default 0.85, determines the extent of strengthening of electrostatic interactions in the membrane (the smaller, the stronger). This parameter was empirically adjusted to give reasonable membrane insertion energies for model systems.

Uncommenting the commented line and adding a continuation to the line above allows the inclusion of Gouy Chapman theory adjustments to the membrane. This describes the effect of a static surface charge on the membrane potential. anfr describes the molar fraction of anionic lipids (e.g. a 70/30 mixture of PC/PG corresponds to ANFR 0.3, which is the default). area is the area (Angstrom^2) per lipid (default 70) and offset is the distance of the plane of negative charge, usually the phosphates, from the hydrocarbon/water boundary (default 3). conc and valence is the molarity and valence of the salt (default 0.1 and 1, respectively).

Visualising the Membrane in VMD

VMD can be loaded using the command:

module load vmd/1.8.6

To view the membrane in VMD, first create a file called centre.pdb, with the following line of text:

ATOM      1  Ne      1      0.0  0.0  0.0  1.00  0.00      MAIN

This is simply an Ne atom placed at the origin. Also, obtain plotBox.tcl from the Wales Group homepage [1].

Load VMD and any molecules that you wish to visualise, followed by centre.pdb. Then open up the TK console and type:

source <PATH>/plotBox.tcl
plotBox z 30.0 30.0 13.0 0.0

The syntax of this: z refers to the direction of the surface normal of the membrane. 30.0 and 30.0 specify half the length of the membrane in the x and y directions in angstroms and can be increased if necessary. 13.0 describes half of the width of the membrane and 0.0 refers to the separation of the slab layers.

N.B It is important to load centre and input the commands into the console after all the molecules have been loaded. Otherwise the width of the membrane will be scaled by VMD.