Covalent Library Preparation 2024: Difference between revisions

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Modify warhead to covalent adduct with SiH3 added.
Modify warhead to covalent adduct with SiH3 added.


== Prepare “SMILES ID” file. ==
= Prepare “SMILES ID” file. =


  ssh n-1-17 (or another development node)
  ssh n-1-17 (or another development node)
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* 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




==  3D Covalent Building for SGE ==
=  Submitting 3D Covalent Building Jobs on BKS Cluster  =
== SGE ==
SSH Gimel
SSH Gimel
  ssh gimel (with s_ account)
  ssh gimel (with s_ account)
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Source Environments
Source Environments
  setenv DOCKBASE /nfs/soft/dock/versions/dock37/DOCK-3.7-trunk
  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 ~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
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  csh /nfs/exk/copipeline/0001_wrapper_queue_build_smiles_ligand_mod_corina_covalent.csh input.smi
  csh /nfs/exk/copipeline/0001_wrapper_queue_build_smiles_ligand_mod_corina_covalent.csh input.smi


== 3D Covalent Building for SLURM ==
== SLURM ==
SSH Epyc
  ssh gimel2
  ssh epyc (with s_ account)
  source /nfs/home/khtang/code/Covalent_3dbuilding_dock37/covalent_3dbuild.sh
Set to csh
  sh /nfs/home/khtang/code/Covalent_3dbuilding_dock37/wrapper_covalent_slurm.sh input.smi
  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
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


= Run job locally on CentOS 7 (for small set of molecules) =
  // build covalent db2 file from smiles
  // build covalent db2 file from smiles
source /nfs/home/khtang/code/Covalent_3dbuilding_dock37/covalent_3dbuild.sh
  export SOURCE_FILE=input.smi
  export SOURCE_FILE=input.smi
  bash $DOCKBASE/ligand/generate/build_database_ligand.sh --no-db --no-solv --no-mol2 --single --covalent -H 7.4
  bash $DOCKBASE/ligand/generate/build_database_ligand.sh --no-db --no-solv --no-mol2 --single --covalent -H 7.4


  // build db2 from mol2
  // build db2 from mol2
  bash /nfs/ex7/blaster/templates/build3d_mol2/dock37_pipeline/build_ligand.sh input.mol2 --name="Name" --smiles="SMILES"
  bash $DOCKBASE/build_ligand.sh <mol2_file> --name="Name" --smiles="SMILES"
 
 
   
   
   
   

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"
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