Galaxy | BIOBB | Published Workflow | Protein conformational ensembles generation

Protein conformational ensembles generation

Annotation:

Step	Annotation
Step 1: Pdb output PDB name mypdb.pdb Take tool settings: Manual Input Properties Input: pdb_code 1ake filter [ATOM, MODEL, ENDMDL] api_id pdbe - PDB in Europe REST API
Step 2: ExtractModel input PDB,PDBQT file Output dataset 'output_pdb_path' from step 1 output PDB,PDBQT name myextract_model.pdb Take tool settings: Manual Input Properties Input: models [1] binary_path check_structure output_format pdb
Step 3: ExtractChain input PDB,PDBQT file Output dataset 'output_structure_path' from step 2 output PDB,PDBQT name myextract_monomer.pdb Take tool settings: Manual Input Properties Input: chains ["A"] permissive False binary_path check_structure output_format pdb
Step 4: CpptrajMask input TOP,PDB,PRMTOP,PARMTOP,ZIP file Output dataset 'output_structure_path' from step 3 input MDCRD,CRD,CDF,NETCDF,NC,RESTART,NCRESTART,RESTARTNC,DCD,CHARMM,COR,PDB,MOL2,TRR,GRO,BINPOS,XTC,CIF,ARC,SQM,SDF,CONFLIB file Output dataset 'output_structure_path' from step 3 output MDCRD,CRD,NETCDF,NC,RST7,NCRST,DCD,PDB,MOL2,BINPOS,TRR,XTC,SQM name mycpptraj_mask_backbone.pdb Take tool settings: Manual Input Properties Input: start 1 end -1 steps 1 mask backbone - Backbone atoms format pdb - Protein Data Bank format binary_path cpptraj output_format mdcrd
Step 5: ConcoordDist input PDB,GRO file Output dataset 'output_structure_path' from step 3 output PDB name myconcoord_dist.pdb output GRO name myconcoord_dist.gro output DAT,TXT name myconcoord_dist.dat Take tool settings: Manual Input Properties Input: binary_path dist vdw 1 - OPLS-UA -united atoms- parameters bond_angle 1 - Concoord default parameters retain_hydrogens False nb_interactions False cutoff 4.0 min_distances 50 damp 1.0 fixed_atoms False output_format dat
Step 6: ProdyAnm input PDB file Output dataset 'output_structure_path' from step 3 output PDB name myprody_anm_traj.pdb Take tool settings: Manual Input Properties Input: num_structs 300 selection backbone cutoff 15.0 gamma 1.0 rmsd 2.0
Step 7: ImodImode input PDB file Output dataset 'output_structure_path' from step 3 output DAT,TXT name myimod_imode_evecs.dat Take tool settings: Manual Input Properties Input: cg 2 - Heavy atoms output_format dat
Step 8: CpptrajMask input TOP,PDB,PRMTOP,PARMTOP,ZIP file Output dataset 'output_structure_path' from step 3 input MDCRD,CRD,CDF,NETCDF,NC,RESTART,NCRESTART,RESTARTNC,DCD,CHARMM,COR,PDB,MOL2,TRR,GRO,BINPOS,XTC,CIF,ARC,SQM,SDF,CONFLIB file Output dataset 'output_structure_path' from step 3 output MDCRD,CRD,NETCDF,NC,RST7,NCRST,DCD,PDB,MOL2,BINPOS,TRR,XTC,SQM name mycpptraj_mask_ca.pdb Take tool settings: Manual Input Properties Input: start 1 end -1 steps 1 mask c-alpha - All c-alpha atoms; protein only format pdb - Protein Data Bank format binary_path cpptraj output_format mdcrd
Step 9: ConcoordDisco input PDB file Output dataset 'output_pdb_path' from step 5 input DAT,TXT file Output dataset 'output_dat_path' from step 5 output PDB,XTC,GRO name myconcoord_disco_traj.pdb output DAT name myconcoord_disco_rmsd.dat output PDB name myconcoord_disco_bfactor.pdb Take tool settings: Manual Input Properties Input: binary_path disco vdw 4 - Yamber2 parameters num_structs 300 num_iterations 2500 chirality_check 2 - check on the fly bs 0 nofit False seed 741265 violation 1.0 convergence 50 trials 25 damp 1 - default dyn 1 bump False pairlist_freq 10 cutoff 0.5 ref False scale 1 output_format pdb
Step 10: CpptrajRms input TOP,PDB,PRMTOP,PARMTOP,ZIP file Output dataset 'output_pdb_path' from step 6 input MDCRD,CRD,CDF,NETCDF,NC,RESTART,NCRESTART,RESTARTNC,DCD,CHARMM,COR,PDB,MOL2,TRR,GRO,BINPOS,XTC,CIF,ARC,SQM,SDF,CONFLIB file Output dataset 'output_pdb_path' from step 6 input PDB file Output dataset 'output_structure_path' from step 3 output DAT,AGR,XMGR,GNU name mycpptraj_prody_rms.dat output MDCRD,CRD,CDF,NETCDF,NC,RESTART,NCRESTART,RESTARTNC,DCD,CHARMM,COR,PDB,MOL2,TRR,GRO,BINPOS,XTC,CIF,ARC,SQM,SDF,CONFLIB name mycpptraj_rms.mdcrd Take tool settings: Manual Input Properties Input: start 1 end -1 steps 1 mask c-alpha - All c-alpha atoms; protein only reference experimental - Use the experimental structure as reference nofit False norotate False nomod False binary_path cpptraj output_cpptraj_path_format dat output_traj_path_format mdcrd
Step 11: CpptrajConvert input TOP,PDB,PRMTOP,PARMTOP,ZIP file Output dataset 'output_cpptraj_path' from step 4 input MDCRD,CRD,CDF,NETCDF,NC,RESTART,NCRESTART,RESTARTNC,DCD,CHARMM,COR,PDB,MOL2,TRR,GRO,BINPOS,XTC,CIF,ARC,SQM,SDF,CONFLIB file Output dataset 'output_pdb_path' from step 6 output MDCRD,CRD,NETCDF,NC,RST7,NCRST,DCD,PDB,MOL2,BINPOS,TRR,XTC,SQM name mycpptraj_prody_anm_traj.trr Take tool settings: Manual Input Properties Input: start 1 end -1 steps 1 mask c-alpha - All c-alpha atoms; protein only format trr - Trajectory of a simulation experiment used by GROMACS binary_path cpptraj output_format mdcrd
Step 12: ImodImc input PDB file Output dataset 'output_structure_path' from step 3 input DAT,TXT file Output dataset 'output_dat_path' from step 7 output PDB name myimod_imc.pdb Take tool settings: Manual Input Properties Input: num_structs 300 num_modes 10 amplitude 6
Step 13: BdRun input PDB file Output dataset 'output_cpptraj_path' from step 8 output LOG,OUT,TXT,O name mybd_flexserv_bd_ensemble.log output CRD,MDCRD,INPCRD name mybd_flexserv_bd_ensemble.mdcrd Take tool settings: Manual Input Properties Input: binary_path bd time 30000 dt 1e-15 wfreq 100 output_log_path_format log output_crd_path_format crd
Step 14: DmdRun input PDB file Output dataset 'output_cpptraj_path' from step 8 output LOG,OUT,TXT,O name mydmd_flexserv_dmd_ensemble.log output CRD,MDCRD,INPCRD name mydmd_flexserv_dmd_ensemble.mdcrd Take tool settings: Manual Input Properties Input: binary_path dmdgoopt dt 1e-12 temperature 300 frames 300 output_log_path_format log output_crd_path_format crd
Step 15: NolbNma input PDB file Output dataset 'output_cpptraj_path' from step 8 output PDB name mynolb_ensemble.pdb Take tool settings: Manual Input Properties Input: num_structs 300 cutoff 5.0 rmsd 4.0
Step 16: MakeNdx input GRO,PDB,TPR file Output dataset 'output_cpptraj_path' from step 8 input NDX file select at runtime output NDX name mymake_gmx_ndx.ndx Take tool settings: Manual Input Properties Input: selection 3 gmx_lib Empty. binary_path gmx
Step 17: NmaRun input PDB file Output dataset 'output_cpptraj_path' from step 8 output LOG,OUT,TXT,O name mynma_flexserv_nma_ensemble.log output CRD,MDCRD,INPCRD name mynma_flexserv_nma_ensemble.mdcrd Take tool settings: Manual Input Properties Input: binary_path diaghess frames 300 nvecs 50 output_log_path_format log output_crd_path_format crd
Step 18: CpptrajRms input TOP,PDB,PRMTOP,PARMTOP,ZIP file Output dataset 'output_pdb_path' from step 5 input MDCRD,CRD,CDF,NETCDF,NC,RESTART,NCRESTART,RESTARTNC,DCD,CHARMM,COR,PDB,MOL2,TRR,GRO,BINPOS,XTC,CIF,ARC,SQM,SDF,CONFLIB file Output dataset 'output_traj_path' from step 9 input PDB file Output dataset 'output_structure_path' from step 3 output DAT,AGR,XMGR,GNU name mycpptraj_concoord_rmsd.dat output MDCRD,CRD,CDF,NETCDF,NC,RESTART,NCRESTART,RESTARTNC,DCD,CHARMM,COR,PDB,MOL2,TRR,GRO,BINPOS,XTC,CIF,ARC,SQM,SDF,CONFLIB name mycpptraj_rms.mdcrd Take tool settings: Manual Input Properties Input: start 1 end -1 steps 1 mask c-alpha - All c-alpha atoms; protein only reference experimental - Use the experimental structure as reference nofit False norotate False nomod False binary_path cpptraj output_cpptraj_path_format dat output_traj_path_format mdcrd
Step 19: CpptrajConvert input TOP,PDB,PRMTOP,PARMTOP,ZIP file Output dataset 'output_pdb_path' from step 5 input MDCRD,CRD,CDF,NETCDF,NC,RESTART,NCRESTART,RESTARTNC,DCD,CHARMM,COR,PDB,MOL2,TRR,GRO,BINPOS,XTC,CIF,ARC,SQM,SDF,CONFLIB file Output dataset 'output_traj_path' from step 9 output MDCRD,CRD,NETCDF,NC,RST7,NCRST,DCD,PDB,MOL2,BINPOS,TRR,XTC,SQM name mycpptraj_disco_traj.trr Take tool settings: Manual Input Properties Input: start 1 end -1 steps 1 mask c-alpha - All c-alpha atoms; protein only format trr - Trajectory of a simulation experiment used by GROMACS binary_path cpptraj output_format mdcrd
Step 20: CpptrajRms input TOP,PDB,PRMTOP,PARMTOP,ZIP file Output dataset 'output_traj_path' from step 12 input MDCRD,CRD,CDF,NETCDF,NC,RESTART,NCRESTART,RESTARTNC,DCD,CHARMM,COR,PDB,MOL2,TRR,GRO,BINPOS,XTC,CIF,ARC,SQM,SDF,CONFLIB file Output dataset 'output_traj_path' from step 12 input PDB file Output dataset 'output_structure_path' from step 3 output DAT,AGR,XMGR,GNU name mycpptraj_rms.dat output MDCRD,CRD,CDF,NETCDF,NC,RESTART,NCRESTART,RESTARTNC,DCD,CHARMM,COR,PDB,MOL2,TRR,GRO,BINPOS,XTC,CIF,ARC,SQM,SDF,CONFLIB name mycpptraj_rms.mdcrd Take tool settings: Manual Input Properties Input: start 1 end -1 steps 1 mask c-alpha - All c-alpha atoms; protein only reference experimental - Use the experimental structure as reference nofit False norotate False nomod False binary_path cpptraj output_cpptraj_path_format dat output_traj_path_format mdcrd
Step 21: CpptrajConvert input TOP,PDB,PRMTOP,PARMTOP,ZIP file Output dataset 'output_traj_path' from step 12 input MDCRD,CRD,CDF,NETCDF,NC,RESTART,NCRESTART,RESTARTNC,DCD,CHARMM,COR,PDB,MOL2,TRR,GRO,BINPOS,XTC,CIF,ARC,SQM,SDF,CONFLIB file Output dataset 'output_traj_path' from step 12 output MDCRD,CRD,NETCDF,NC,RST7,NCRST,DCD,PDB,MOL2,BINPOS,TRR,XTC,SQM name mycpptraj_imods_ensemble.trr Take tool settings: Manual Input Properties Input: start 1 end -1 steps 1 mask c-alpha - All c-alpha atoms; protein only format trr - Trajectory of a simulation experiment used by GROMACS binary_path cpptraj output_format mdcrd
Step 22: CpptrajRms input TOP,PDB,PRMTOP,PARMTOP,ZIP file Output dataset 'output_cpptraj_path' from step 8 input MDCRD,CRD,CDF,NETCDF,NC,RESTART,NCRESTART,RESTARTNC,DCD,CHARMM,COR,PDB,MOL2,TRR,GRO,BINPOS,XTC,CIF,ARC,SQM,SDF,CONFLIB file Output dataset 'output_crd_path' from step 13 input PDB file Output dataset 'output_structure_path' from step 3 output DAT,AGR,XMGR,GNU name mycpptraj_flexserv_bd_rmsd.dat output MDCRD,CRD,CDF,NETCDF,NC,RESTART,NCRESTART,RESTARTNC,DCD,CHARMM,COR,PDB,MOL2,TRR,GRO,BINPOS,XTC,CIF,ARC,SQM,SDF,CONFLIB name mycpptraj_flexserv_bd_traj_fitted.trr Take tool settings: Manual Input Properties Input: start 1 end -1 steps 1 mask c-alpha - All c-alpha atoms; protein only reference experimental - Use the experimental structure as reference nofit False norotate False nomod False binary_path cpptraj output_cpptraj_path_format dat output_traj_path_format mdcrd
Step 23: CpptrajRms input TOP,PDB,PRMTOP,PARMTOP,ZIP file Output dataset 'output_cpptraj_path' from step 8 input MDCRD,CRD,CDF,NETCDF,NC,RESTART,NCRESTART,RESTARTNC,DCD,CHARMM,COR,PDB,MOL2,TRR,GRO,BINPOS,XTC,CIF,ARC,SQM,SDF,CONFLIB file Output dataset 'output_crd_path' from step 14 input PDB file Output dataset 'output_structure_path' from step 3 output DAT,AGR,XMGR,GNU name mycpptraj_flexserv_dmd_rmsd.dat output MDCRD,CRD,CDF,NETCDF,NC,RESTART,NCRESTART,RESTARTNC,DCD,CHARMM,COR,PDB,MOL2,TRR,GRO,BINPOS,XTC,CIF,ARC,SQM,SDF,CONFLIB name mycpptraj_flexserv_dmd_traj_fitted.trr Take tool settings: Manual Input Properties Input: start 1 end -1 steps 1 mask c-alpha - All c-alpha atoms; protein only reference experimental - Use the experimental structure as reference nofit False norotate False nomod False binary_path cpptraj output_cpptraj_path_format dat output_traj_path_format trr
Step 24: CpptrajRms input TOP,PDB,PRMTOP,PARMTOP,ZIP file Output dataset 'output_cpptraj_path' from step 8 input MDCRD,CRD,CDF,NETCDF,NC,RESTART,NCRESTART,RESTARTNC,DCD,CHARMM,COR,PDB,MOL2,TRR,GRO,BINPOS,XTC,CIF,ARC,SQM,SDF,CONFLIB file Output dataset 'output_pdb_path' from step 15 input PDB file Output dataset 'output_structure_path' from step 3 output DAT,AGR,XMGR,GNU name mycpptraj_nolb_rmsd.dat output MDCRD,CRD,CDF,NETCDF,NC,RESTART,NCRESTART,RESTARTNC,DCD,CHARMM,COR,PDB,MOL2,TRR,GRO,BINPOS,XTC,CIF,ARC,SQM,SDF,CONFLIB name mycpptraj_rms.mdcrd Take tool settings: Manual Input Properties Input: start 1 end -1 steps 1 mask c-alpha - All c-alpha atoms; protein only reference experimental - Use the experimental structure as reference nofit False norotate False nomod False binary_path cpptraj output_cpptraj_path_format dat output_traj_path_format mdcrd
Step 25: CpptrajConvert input TOP,PDB,PRMTOP,PARMTOP,ZIP file Output dataset 'output_cpptraj_path' from step 8 input MDCRD,CRD,CDF,NETCDF,NC,RESTART,NCRESTART,RESTARTNC,DCD,CHARMM,COR,PDB,MOL2,TRR,GRO,BINPOS,XTC,CIF,ARC,SQM,SDF,CONFLIB file Output dataset 'output_pdb_path' from step 15 output MDCRD,CRD,NETCDF,NC,RST7,NCRST,DCD,PDB,MOL2,BINPOS,TRR,XTC,SQM name mycpptraj_nolb_ensemble.trr Take tool settings: Manual Input Properties Input: start 1 end -1 steps 1 mask c-alpha - All c-alpha atoms; protein only format trr - Trajectory of a simulation experiment used by GROMACS binary_path cpptraj output_format trr
Step 26: CpptrajRms input TOP,PDB,PRMTOP,PARMTOP,ZIP file Output dataset 'output_cpptraj_path' from step 8 input MDCRD,CRD,CDF,NETCDF,NC,RESTART,NCRESTART,RESTARTNC,DCD,CHARMM,COR,PDB,MOL2,TRR,GRO,BINPOS,XTC,CIF,ARC,SQM,SDF,CONFLIB file Output dataset 'output_crd_path' from step 17 input PDB file Output dataset 'output_structure_path' from step 3 output DAT,AGR,XMGR,GNU name mycpptraj_flexserv_nma_rmsd.dat output MDCRD,CRD,CDF,NETCDF,NC,RESTART,NCRESTART,RESTARTNC,DCD,CHARMM,COR,PDB,MOL2,TRR,GRO,BINPOS,XTC,CIF,ARC,SQM,SDF,CONFLIB name mycpptraj_rms.mdcrd Take tool settings: Manual Input Properties Input: start 1 end -1 steps 1 mask c-alpha - All c-alpha atoms; protein only reference experimental - Use the experimental structure as reference nofit False norotate False nomod False binary_path cpptraj output_cpptraj_path_format dat output_traj_path_format mdcrd
Step 27: CpptrajConvert input TOP,PDB,PRMTOP,PARMTOP,ZIP file Output dataset 'output_cpptraj_path' from step 8 input MDCRD,CRD,CDF,NETCDF,NC,RESTART,NCRESTART,RESTARTNC,DCD,CHARMM,COR,PDB,MOL2,TRR,GRO,BINPOS,XTC,CIF,ARC,SQM,SDF,CONFLIB file Output dataset 'output_crd_path' from step 17 output MDCRD,CRD,NETCDF,NC,RST7,NCRST,DCD,PDB,MOL2,BINPOS,TRR,XTC,SQM name mycpptraj_flexserv_nma_ensemble.trr Take tool settings: Manual Input Properties Input: start 1 end -1 steps 1 mask c-alpha - All c-alpha atoms; protein only format trr - Trajectory of a simulation experiment used by GROMACS binary_path cpptraj output_format mdcrd
Step 28: Zip File to zips File to zip 1 Zipped file name (without spaces) mycpptraj_prody_anm_traj.trr File Output dataset 'output_cpptraj_path' from step 11 File to zip 2 Zipped file name (without spaces) mycpptraj_disco_traj.trr File Output dataset 'output_cpptraj_path' from step 19 File to zip 3 Zipped file name (without spaces) mycpptraj_flexserv_dmd_traj_fitted.trr File Output dataset 'output_traj_path' from step 23 File to zip 4 Zipped file name (without spaces) mycpptraj_imods_ensemble.trr File Output dataset 'output_cpptraj_path' from step 21 File to zip 5 Zipped file name (without spaces) mycpptraj_flexserv_nma_ensemble.trr File Output dataset 'output_cpptraj_path' from step 27
Step 29: Trjcat input ZIP file Output dataset 'output' from step 28 output PDB,GRO,XTC,TRR,TNG name mytrjcat_concat_traj.trr Take tool settings: Manual Input Properties Input: concatenate True gmx_lib Empty. binary_path gmx output_format pdb
Step 30: GmxCluster input TPR,GRO,G96,PDB,BRK,ENT file Output dataset 'output_cpptraj_path' from step 8 input XTC,TRR,CPT,GRO,G96,PDB,TNG file Output dataset 'output_trj_path' from step 29 input NDX file Output dataset 'output_ndx_path' from step 16 output XTC,TRR,CPT,GRO,G96,PDB,TNG name mygmx_concat.cluster.pdb output LOG name mygmx_cluster.log output XPM name mygmx_cluster.xpm output XVG name mygmx_cluster.xvg Take tool settings: Manual Input Properties Input: fit_selection System - all atoms in the system output_selection System - all atoms in the system dista False nofit False method linkage - Add a structure to a cluster when its distance to any element of the cluster is less than cutoff cutoff 0.12 binary_path gmx output_format xtc
Step 31: CpptrajRms input TOP,PDB,PRMTOP,PARMTOP,ZIP file Output dataset 'output_cpptraj_path' from step 8 input MDCRD,CRD,CDF,NETCDF,NC,RESTART,NCRESTART,RESTARTNC,DCD,CHARMM,COR,PDB,MOL2,TRR,GRO,BINPOS,XTC,CIF,ARC,SQM,SDF,CONFLIB file Output dataset 'output_pdb_path' from step 30 input PDB file Output dataset 'output_cpptraj_path' from step 8 output DAT,AGR,XMGR,GNU name mycpptraj_meta_traj_rmsd.dat output MDCRD,CRD,CDF,NETCDF,NC,RESTART,NCRESTART,RESTARTNC,DCD,CHARMM,COR,PDB,MOL2,TRR,GRO,BINPOS,XTC,CIF,ARC,SQM,SDF,CONFLIB name mycpptraj_meta_traj_fitted.crd Take tool settings: Manual Input Properties Input: start 1 end -1 steps 1 mask c-alpha - All c-alpha atoms; protein only reference experimental - Use the experimental structure as reference nofit False norotate False nomod False binary_path cpptraj output_cpptraj_path_format dat output_traj_path_format mdcrd
Step 32: PczZip input PDB file Output dataset 'output_cpptraj_path' from step 8 input CRD,MDCRD,INPCRD file Output dataset 'output_traj_path' from step 31 output PCZ name mypcz_concat_ensemble.pcz Take tool settings: Manual Input Properties Input: binary_path pcazip neigenv 10 variance 90 verbose False gauss_rmsd False
Step 33: PczZip input PDB file Output dataset 'output_cpptraj_path' from step 8 input CRD,MDCRD,INPCRD file Output dataset 'output_traj_path' from step 31 output PCZ name mypcz_concat_ensemble_gaussian.pcz Take tool settings: Manual Input Properties Input: binary_path pcazip neigenv 10 variance 90 verbose False gauss_rmsd True
Step 34: PczInfo input PCZ file Output dataset 'output_pcz_path' from step 32 output JSON name mypcz_report.json Take tool settings: Manual Input Properties Input: binary_path pczdump
Step 35: PczEvecs input PCZ file Output dataset 'output_pcz_path' from step 32 output JSON name mypcz_evecs.json Take tool settings: Manual Input Properties Input: binary_path pczdump eigenvector 1
Step 36: PczAnimate input PCZ file Output dataset 'output_pcz_path' from step 32 output CRD,MDCRD,INPCRD,PDB name mypcz_proj1.crd Take tool settings: Manual Input Properties Input: binary_path pczdump eigenvector 1 pdb False output_format crd
Step 37: PczBfactor input PCZ file Output dataset 'output_pcz_path' from step 32 output DAT,TXT,CSV name mypcz_bfactor_all.dat output PDB name mypcz_bfactor_all.pdb Take tool settings: Manual Input Properties Input: binary_path pczdump eigenvector 0 pdb True output_format dat
Step 38: PczStiffness input PCZ file Output dataset 'output_pcz_path' from step 32 output JSON name mypcz_stiffness.json Take tool settings: Manual Input Properties Input: binary_path pczdump eigenvector 0 temperature 300
Step 39: PczCollectivity input PCZ file Output dataset 'output_pcz_path' from step 32 output JSON name mypcz_collectivity.json Take tool settings: Manual Input Properties Input: eigenvector 0 binary_path pczdump
Step 40: PczHinges input PCZ file Output dataset 'output_pcz_path' from step 33 output JSON name mypcz_hinges_bfactor_report.json Take tool settings: Manual Input Properties Input: binary_path pczdump eigenvector 0 method Bfactor_slope
Step 41: PczHinges input PCZ file Output dataset 'output_pcz_path' from step 33 output JSON name mypcz_hinges_dyndom_report.json Take tool settings: Manual Input Properties Input: binary_path pczdump eigenvector 0 method Dynamic_domain
Step 42: PczHinges input PCZ file Output dataset 'output_pcz_path' from step 33 output JSON name mypcz_hinges_fcte_report.json Take tool settings: Manual Input Properties Input: binary_path pczdump eigenvector 0 method Force_constant
Step 43: CpptrajConvert input TOP,PDB,PRMTOP,PARMTOP,ZIP file Output dataset 'output_cpptraj_path' from step 8 input MDCRD,CRD,CDF,NETCDF,NC,RESTART,NCRESTART,RESTARTNC,DCD,CHARMM,COR,PDB,MOL2,TRR,GRO,BINPOS,XTC,CIF,ARC,SQM,SDF,CONFLIB file Output dataset 'output_crd_path' from step 36 output MDCRD,CRD,NETCDF,NC,RST7,NCRST,DCD,PDB,MOL2,BINPOS,TRR,XTC,SQM name mycpptraj_pcz_proj1.dcd Take tool settings: Manual Input Properties Input: start 1 end -1 steps 1 mask all-atoms - All system atoms format dcd - AMBER trajectory format binary_path cpptraj output_format dcd

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Protein conformational ensembles generation

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