Covalent Library Preparation 2024: Difference between revisions
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(Created page with "Modify warhead to covalent adduct with SiH3 added. == Prepare “SMILES ID” file. == ssh n-1-17 (or another development node) Source environment with RDkit source /mnt/nfs/ex9/work/ttummino/miniconda/etc/profile.d/conda.sh conda activate base3.7 python ~ak87/PROGRAM/convert_smiles_to_covalent.py ald bbv-cov-ald.smi bbv-cov-ald-test.smi This script enumerates all stereoisomers and converts SMILES to the covalent ones. Currently, only conversions for aldehydes...") |
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Modify warhead to covalent adduct with SiH3 added. | Modify warhead to covalent adduct with SiH3 added. | ||
= Prepare “SMILES ID” file. = | |||
ssh n-1-17 (or another development node) | ssh n-1-17 (or another development node) | ||
| Line 20: | Line 20: | ||
* Third arg: output file name | * Third arg: output file name | ||
== 3D Covalent Building for Wynton == | |||
Set to csh | |||
csh | |||
Source Environments | |||
setenv DOCKBASE /wynton/group/bks/CovalentBuilding/DOCK-3.7-trunk | |||
source /wynton/group/bks/CovalentBuilding/.csh_corina | |||
source /wynton/group/bks/CovalentBuilding/DOCK-3.7-trunk/env.csh | |||
Run Script with input.smi as your prepared SMILES file | |||
csh /wynton/group/bks/CovalentBuilding/0001_wrapper_queue_build_smiles_ligand_mod_corina_covalent.csh input.smi | |||
== | = Submitting 3D Covalent Building Jobs on BKS Cluster = | ||
== SGE == | |||
SSH Gimel | SSH Gimel | ||
ssh gimel | ssh gimel (with s_ account) | ||
Set to csh | Set to csh | ||
csh | csh | ||
Source Environments | Source Environments | ||
setenv DOCKBASE /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk | |||
source ~elisfink/.csh_corina | source ~elisfink/.csh_corina | ||
source /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/env.csh | source /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/env.csh | ||
it is in the /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/env.csh | |||
Run Script with input.smi as your prepared SMILES file | Run Script with input.smi as your prepared SMILES file | ||
csh | csh /nfs/exk/copipeline/0001_wrapper_queue_build_smiles_ligand_mod_corina_covalent.csh input.smi | ||
== SLURM == | |||
ssh gimel2 | |||
source /nfs/home/khtang/code/Covalent_3dbuilding_dock37/covalent_3dbuild.sh | |||
sh /nfs/home/khtang/code/Covalent_3dbuilding_dock37/wrapper_covalent_slurm.sh input.smi | |||
= Run job locally on CentOS 7 (for small set of molecules) = | |||
// build covalent db2 file from smiles | |||
source /nfs/home/khtang/code/Covalent_3dbuilding_dock37/covalent_3dbuild.sh | |||
export SOURCE_FILE=input.smi | |||
bash $DOCKBASE/ligand/generate/build_database_ligand.sh --no-db --no-solv --no-mol2 --single --covalent -H 7.4 | |||
// build db2 from mol2 | |||
bash $DOCKBASE/build_ligand.sh <mol2_file> --name="Name" --smiles="SMILES" | |||
[[Category:Covalent]] | [[Category:Covalent]] | ||
Latest revision as of 19:58, 11 February 2025
Modify warhead to covalent adduct with SiH3 added.
Prepare “SMILES ID” file.
ssh n-1-17 (or another development node)
Source environment with RDkit
source /mnt/nfs/ex9/work/ttummino/miniconda/etc/profile.d/conda.sh
conda activate base3.7
python ~ak87/PROGRAM/convert_smiles_to_covalent.py ald bbv-cov-ald.smi bbv-cov-ald-test.smi
This script enumerates all stereoisomers and converts SMILES to the covalent ones. Currently, only conversions for aldehydes and nitriles is supported. Usage:
- First arg: ald or nitr for aldehyde or nitrile
- Second arg: input smi file
- Third arg: output file name
3D Covalent Building for Wynton
Set to csh
csh
Source Environments
setenv DOCKBASE /wynton/group/bks/CovalentBuilding/DOCK-3.7-trunk source /wynton/group/bks/CovalentBuilding/.csh_corina source /wynton/group/bks/CovalentBuilding/DOCK-3.7-trunk/env.csh
Run Script with input.smi as your prepared SMILES file
csh /wynton/group/bks/CovalentBuilding/0001_wrapper_queue_build_smiles_ligand_mod_corina_covalent.csh input.smi
Submitting 3D Covalent Building Jobs on BKS Cluster
SGE
SSH Gimel
ssh gimel (with s_ account)
Set to csh
csh
Source Environments
setenv DOCKBASE /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk source ~elisfink/.csh_corina source /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/env.csh
it is in the /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/env.csh Run Script with input.smi as your prepared SMILES file
csh /nfs/exk/copipeline/0001_wrapper_queue_build_smiles_ligand_mod_corina_covalent.csh input.smi
SLURM
ssh gimel2 source /nfs/home/khtang/code/Covalent_3dbuilding_dock37/covalent_3dbuild.sh sh /nfs/home/khtang/code/Covalent_3dbuilding_dock37/wrapper_covalent_slurm.sh input.smi
Run job locally on CentOS 7 (for small set of molecules)
// build covalent db2 file from smiles source /nfs/home/khtang/code/Covalent_3dbuilding_dock37/covalent_3dbuild.sh export SOURCE_FILE=input.smi bash $DOCKBASE/ligand/generate/build_database_ligand.sh --no-db --no-solv --no-mol2 --single --covalent -H 7.4
// build db2 from mol2 bash $DOCKBASE/build_ligand.sh <mol2_file> --name="Name" --smiles="SMILES"