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[求助]
关于用DS做虚拟筛选的问题
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| 我想用DS中的ligandfit这个模块进行虚拟筛选，但是每次运行一分钟之后就提示错误，想请大侠指点一下能否使用这个模块进行筛选，需要注意的问题是什么，谢谢 |
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blue_cat
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2楼2012-09-23 15:29:59
3楼2012-09-23 16:51:42
blue_cat
木虫 (正式写手)
- 模拟EPI: 1
- 应助: 50 (小学生)
- 金币: 4438.3
- 红花: 11
- 帖子: 696
- 在线: 104.7小时
- 虫号: 983443
- 注册: 2010-03-27
- 性别: GG
- 专业: 药物化学
4楼2012-09-24 12:59:27
|
Dock Ligands (LigandFit) ________________________________________ Description Docks ligands into an active site using a shape filter and Monte-Carlo ligand conformation generation. Uses LigandFit Monte-Carlo techniques to generate ligand conformations and docks them into the active site using a shape-based initial docking. The docked poses may optionally be minimized with CHARMm and evaluated with a set of scoring functions. The following steps are performed: 1. Performs ligand docking using LigandFit 2. Minimizes docked poses using CHARMm 3. Scores poses Steps in italics may be skipped depending on settings Information Name Dock Ligands (LigandFit) Status Error User accelrys System localhost (Linux32) Start Time 2007-09-08 13:45:35 Finish Time 2007-09-08 13:46:21 Execution Time 00:00:46 Error Messages Job 'Docking' Failed Input Files Dock Ligands (LigandFit) Protocol Protocol.pr_xml Input Binding Site BindingSite.txt Input Control Ligands Molecule.sd Input Receptor 2CLQ.msv Output Files Dock Ligands (LigandFit) Log Output.log Failed Ligands (LigandFit docking) SPECS10000_dock_fail.sd LigandFit Log LigandFit-2CLQ.log Summary 10001 input ligands 1 poses were filtered or failed to dock no ligands docked Parameters Input Receptor ../Input/2CLQ.msv Input Binding Site ../Input/BindingSite.txt Input Ligands /home/accelrys/DSResult/PPENG/SPECS10000.sdf Input Control Ligands ../Input/Molecule.sd Input Preserve Controls In Input True Input Control Ligand Property Control Energy Grid Dreiding Energy Grid Extension from Site 3.0 Energy Grid Outside Binding Site Penalty 0.0 Energy Grid Softened Potential Energy True Energy Grid Dielectric Constant 1.0 Energy Grid Nonbonded Cutoff Distance 10.0 Energy Grid Distance Dependent Dielectric True Number of Monte Carlo Trials "2 500 120, 4 1200 300, 6 1500 350, 10 2000 500, 25 3000 750" Conformation Search Conformation Search Include Electrostatic Energy False Conformation Search Torsional Step Size for Polar H 30.0 Conformation Search Maximum Internal Energy 10000.00 Docking Docking Docking RMS Threshold for Ligand/Site Match 2.0 Docking Site Fusing RMS Cutoff Docking Rigid Body SD Iterations 10 Docking Rigid Body BFGS Iterations 20 Maximum Poses Retained 10 Pose Saving Pose Saving DockScore Threshold 0.0 Pose Saving Rigid Body BFGS Iterations 0 Pose Saving RMS Threshold for Diversity 1.50 Pose Saving Score Threshold for Diversity 20.0 Pose Saving Perform Clustering False Pose Saving Maximum Clusters per Molecule 5 Pose Saving RMS Threshold for Clustering 1.5 Interaction Filters Interaction Filters Minimum Number of Features 0 Interaction Filters Donor Include SH True Interaction Filters Acceptor Include Aromatic F True Interaction Filters Metal include S True Interaction Filters Save Only Poses with Minimum Features False Minimization Algorithm Do not minimize Minimization Sphere of Flexible Atoms Minimization Forcefield CHARMm Minimization Iterations 1000 Minimization Dielectric Constant 1.0 Minimization Distant-Dependent Dielectrics True Minimization Energy Tolerance 0.0 Minimization Gradient Tolerance 0.001 Minimization Nonbond Cutoff 13.0 Scoring Functions LigScore1, LigScore2, PLP1, PLP2, Jain, PMF LigScore Scoring LigScore Forcefield Dreiding Scoring LigScore Energy Grid Extension 5.0 Scoring LigScore1 Label LigScore1 Scoring LigScore1 Minimum Score Scoring LigScore1 Report Individual Contributions False Scoring LigScore2 Label LigScore2 Scoring LigScore2 Minimum Score Scoring LigScore2 Report Individual Contributions False PLP Scoring PLP1 Label -PLP1 Scoring PLP1 Minimum Negative Score Scoring PLP2 Label -PLP2 Scoring PLP2 Minimum Negative Score Jain Scoring Jain Label Jain Scoring Jain Minimum Score Scoring Jain Ignore Non-Polar Hydrogens False Scoring Jain Ignore Water False PMF Scoring PMF Label -PMF Scoring PMF Minimum Negative Score Scoring PMF Ignore Hydrogens True Scoring PMF Other Interactions Cutoff 12.0 Scoring PMF Carbon-Carbon Cutoff 12.0 PMF04 Scoring PMF04 Label -PMF04 Scoring PMF04 Minimum Negative Score Scoring PMF04 Ignore Hydrogens True Scoring PMF04 Carbon-Carbon Cutoff 6.0 Scoring PMF04 Other Interactions Cutoff 9.0 Ludi Scoring Ludi Score Label Ludi Scoring Ludi 1 Minimum Score Scoring Ludi 2 Minimum Score Scoring Ludi 3 Minimum Score Scoring Ludi Report Individual Contributions False Rotated Atoms Property Receptor.Positions, Gold.Protein.RotatedAtoms Parallel Processing False Parallel Processing Batch Size 25 Parallel Processing Server localhost Parallel Processing Server Processes 2 Parallel Processing Preserve Order True 以上这是所有的信息了，希望大侠能帮我解决，感激不尽 |
5楼2012-09-24 15:42:34