Difference between revisions of "Connecting two minima with a pathway"
Jump to navigation
Jump to search
import>Jmc49 (New page: This tutorial takes two PDB structures for the ALA-PHE dipeptide (generated with LEaP and GMIN or from another source), and runs through setting up how to connect them with a connected...) |
import>Csw34 |
||
| Line 1: | Line 1: | ||
| + | There are two versions of this tutorial, one for AMBER users, using A9OPTIM, and one for CHARMM users, using COPTIM. |
||
| + | |||
| + | == AMBER (A9OPTIM) version == |
||
This tutorial takes two PDB structures for the ALA-PHE dipeptide (generated with LEaP and [[GMIN]] or from another source), and runs through setting up how to connect them with a connected pathway of minima and transition states using [[OPTIM]] and AMBER9 (A9OPTIM). |
This tutorial takes two PDB structures for the ALA-PHE dipeptide (generated with LEaP and [[GMIN]] or from another source), and runs through setting up how to connect them with a connected pathway of minima and transition states using [[OPTIM]] and AMBER9 (A9OPTIM). |
||
| Line 6: | Line 9: | ||
* [[Alternatively, making the initial path with PATHSAMPLE itself]] |
* [[Alternatively, making the initial path with PATHSAMPLE itself]] |
||
* [[Expanding the kinetic transition network with PATHSAMPLE]] |
* [[Expanding the kinetic transition network with PATHSAMPLE]] |
||
| + | |||
| + | == CHARMM (COPTIM version) == |
||
| + | This tutorial takes two structures for the met-enkephalin neurotransmitter peptide, generated using [[GMIN]], and runs through setting up how to connect them with a connected pathway of minima and transition states using [[OPTIM]] and CHARMM (COPTIM). |
||
| + | |||
| + | * [[Setting up (CHARMM)]] |
||
| + | * [[Using GMIN to generate endpoints (CHARMM)]] |
||
| + | * [[Finding an initial path with OPTIM and starting up PATHSAMPLE (CHARMM)]] |
||
| + | * [[Alternatively, making the initial path with PATHSAMPLE itself (CHARMM)]] |
||
| + | * [[Expanding the kinetic transition network with PATHSAMPLE (CHARMM)]] |
||
Revision as of 12:44, 7 February 2012
There are two versions of this tutorial, one for AMBER users, using A9OPTIM, and one for CHARMM users, using COPTIM.
AMBER (A9OPTIM) version
This tutorial takes two PDB structures for the ALA-PHE dipeptide (generated with LEaP and GMIN or from another source), and runs through setting up how to connect them with a connected pathway of minima and transition states using OPTIM and AMBER9 (A9OPTIM).
- Setting up
- Using GMIN to generate endpoints
- Finding an initial path with OPTIM and starting up PATHSAMPLE
- Alternatively, making the initial path with PATHSAMPLE itself
- Expanding the kinetic transition network with PATHSAMPLE
CHARMM (COPTIM version)
This tutorial takes two structures for the met-enkephalin neurotransmitter peptide, generated using GMIN, and runs through setting up how to connect them with a connected pathway of minima and transition states using OPTIM and CHARMM (COPTIM).