Created swapping example #104
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| LIGAND2_ATOMS = <LIG2ATOMS> | ||
| LIGAND1_CM_ATOMS = <LIG1CMATOMS> | ||
| LIGAND2_CM_ATOMS = <LIG2CMATOMS> | ||
| DISPL0_LIG1 = ' 0.0, 0.0, 0.0 ' |
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DISPL0_LIG1 and DISPL0_LIG2 are not relevant for this example. Please remove them.
| ACORE = 0.062500 | ||
| UBCORE = 100.0 | ||
| FRICTION_COEFF = 0.500000 | ||
| HMASS = 1.5 |
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Hydrogen mass repartitioning is carried out in the make_atm_system_from_rcpt_lig.py utility. Please remove HMASS from the input control file.
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| localhost,0:0,1,OpenCL,,/tmp | |||
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Remove nodefile. It is created automatically by the "run" script.
| #SBATCH --no-requeue | ||
| #SBATCH -t 12:00:00 | ||
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| . /nfs/sazimi-d/miniforge3/bin/activate atm8.2.0 |
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Please generalize to:
. $HOME/miniforge3/bin/activate atm8.2.1
the latest release is 8.2.1
| for pair in <LIGPAIRS> ; do | ||
| jobname=<RECEPTOR>-$pair | ||
| echo "Prepping $jobname" | ||
| ( cd ${jobname} && python <ASYNCRE_DIR>/rbfe_structprep.py ${jobname}_asyncre.cntl ) || exit 1 |
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If the user follows the default installation instructions, the rbfe_structprep.py script is installed in the conda environment as an executable:
( cd ${jobname} && rbfe_structprep.py ${jobname}_asyncre.cntl ) || exit 1
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| jobname=<JOBNAME> | ||
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| . /nfs/sazimi-d/miniforge3/bin/activate atm8.2.0 |
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Similarly to the above:
. $HOME/miniforge3/bin/activate atm8.2.1
rbfe_structprep.py ${jobname}_asyncre.cntl || exit 1
rbfe_explicit.py ${jobname}_asyncre.cntl
| #displacement vector | ||
| displacement=("0.0" "70.0" "0.0") | ||
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| #residue ids of the receptor that define the center of the binding site |
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Comment that the example does not use binding site restraints
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| # cat r*/*.out > data | |||
| # R CMD BATCH uwham_analysis.R | |||
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I think we have improved versions of the uwham_analysis.R script that properly label axes in plots and flag large perturbation energy gaps.
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| # Usage: python make_atm_rbfe_system_frompdb.py <options> | ||
| # Emilio Gallicchio, 5/2023 adapted from code by Bill Swope, 11/2021 | ||
| # modified by Solmaz Azimi 6/2024 |
make_atm_system_from_rcpt_lig.py
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| bbox = boundingBoxSizes(rcpt_positions + lig1_positions + lig2_positions) | ||
| bboxsizes = [ bbox[i][1]-bbox[i][0] for i in range(3) ] | ||
| padding = 2. * 1.0*nanometer | ||
| padding = 5. * 1.0*nanometer |
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The padding is significantly larger. Why is this big? Should it be an optional parameter?
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@solmazimi, please address the comment above.
Signed-off-by: Solmaz Azimi <solmazimi@Solmazs-MacBook-Air.local>
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@solmazimi please sync your branch with the current master branch and resolve the conflict with |
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Included receptor and ligand files, and common scripts directory that supports RBFE and swapping calculations