Covalent Library Preparation 2024

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 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

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

3D Covalent Building for SLURM

SSH n-1-19

ssh n-1-19 (with s_ account)

Set to csh

csh

Source Environments

setenv DOCKBASE /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk
setenv AMSOLEXE /nfs/soft/amsol/in-house/amsol7.1-colinear-fix/amsol7.1
source ~elisfink/.csh_corina
source /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_slurm.csh input.smi

Updated version from Khanh

Note: I tried following the pipeline above. Although it worked great on gimel (a CentOS server), I have trouble running it on CentOS 7 servers due to AMSOL that it used which was compiled on a very out-of-date fortran complier. So I recompiled AMSOL and refactored the build3d pipeline to use Python3 (I know, another copy of DOCK that is untracked)

Usage

This script only works on servers with GCC version 4+ (slurm nodes) and it won't work on our sge nodes running on CentOS 6 Example:

ssh n-1-17

source /nfs/ex7/blaster/templates/build3d_mol2/dock37_pipeline/env.sh

// build covalent db2 file from smiles
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 /nfs/ex7/blaster/templates/build3d_mol2/dock37_pipeline/build_ligand.sh input.mol2 --name="Name" --smiles="SMILES"