Difference between revisions of "Running a Go model with the AMHGMIN"
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Moving these files around is defined in the shell scripts, so it does not take any human intervention. |
Moving these files around is defined in the shell scripts, so it does not take any human intervention. |
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| − | ===CHARMM keywords=== |
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| − | The toppar parameters that should be used are the EEF1.1.inp files. This is done using: |
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| − | <pre> |
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| − | open read unit 11 card name toph19_eef1.1.inp |
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| − | read rtf card unit 11 |
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| − | close unit 11 |
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| − | open read unit 12 card name param19_eef1.1.inp |
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| − | read para card unit 12 |
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| − | close unit 12 |
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| − | </pre> |
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| − | The charmm keywords are as follows: |
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| − | <pre> |
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| − | eef1 setup membrane slvt water slv2 chex nsmth 10 width 26.0 temp 298.15 - |
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| − | unit 93 name "/home/jwll2/svn/CHARMM31/toppar/solvpar.1.inp" aemp 0.85 |
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| − | !gouy anfr 0.3 area 70. conc 0.1 offset 3.0 valence 1 |
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| − | update ctonnb 7. ctofnb 9. cutnb 15. group rdie |
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| − | </pre> |
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| − | <b>membrane</b> introduces the membrane model and <b>slvt water</b> and <b>slv2 chex</b> specify that the exterior solvent is water and that the interior solvent is cyclohexane. <b>nsmith</b>, set to 10 as a default, determines how steep the transition is at the interface between interior and exterior. The <b>width</b> 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 <b>aemp</b>, 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. |
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| − | 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. <b>anfr</b> 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). <b>area</b> is the area (Angstrom^2) per lipid (default 70) and <b>offset</b> is the distance of the plane of negative charge, usually the phosphates, from the hydrocarbon/water boundary (default 3). <b>conc</b> and <b>valence</b> is the molarity and valence of the salt (default 0.1 and 1, respectively). |
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Revision as of 13:33, 28 July 2009
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. The format of this file needs to be in the wolynes file format which contains the sequence, the coordinates, the secdondary structure definitions. and the surface accessibility. Converting the file can be done with pdb2wolynes.f program. The file names must be 5 characters where the first 4 are the pdb ID and the final character is the chain within the pdb file.
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. The appropriate gamma.dat file is /home/mp466/amh/md_input/gammas/gamma.go.fourletter.
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.
Moving these files around is defined in the shell scripts, so it does not take any human intervention.