Difference between revisions of "Evaluating different components of AMBER energy function with SANDER"
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import>Mp466 |
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This is easily done. Three input files are needed '''prmtop''', '''inpcrd''', and '''mdin''', along with the SANDER executable. |
This is easily done. Three input files are needed '''prmtop''', '''inpcrd''', and '''mdin''', along with the SANDER executable. |
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| − | -> '''prmtop''' |
+ | -> '''prmtop''' - amber topology file |
| − | (amber topology file) |
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| − | -> '''inpcrd''' |
+ | -> '''inpcrd''' - amber coordinates file |
| − | (amber coordinates file) |
||
| − | -> '''mdin''' |
+ | -> '''mdin''' - SANDER input file |
| − | (SANDER input file) |
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An easy way to do this is create an seperate directory via 'mkdir eval' |
An easy way to do this is create an seperate directory via 'mkdir eval' |
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Revision as of 16:57, 3 October 2009
Editing Evaluating different components of AMBER energy function with SANDER
After running AMBGMIN (with 'DUMPSTRUCTURES', 'SAVE 5' set in GMIN 'data' file), it is informative to examine the different components of the all-atom energy function. The AMBGMIN output contains averages over MD time steps which is not the same at the evaluation of the lowest energy state, naturally. One can use SANDER to run one step of minimisation to generate the different components of the energy function.
This is easily done. Three input files are needed prmtop, inpcrd, and mdin, along with the SANDER executable.
-> prmtop - amber topology file
-> inpcrd - amber coordinates file
-> mdin - SANDER input file
An easy way to do this is create an seperate directory via 'mkdir eval'
1. compile SANDER:
2. move files from GMIN output directory:
cp min1.rst eval/inpcrd
cp coord.prmtop eval/prmtop
cp min.in eval/mdin
3. Run SANDER:
4. output files:
mdinfo - Energy function output only mdout - Total Amber output restrt - coordinates for restarting AMBER