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  1. Run.java.csh‏‎ (16:49, 31 January 2008)
  2. Binding Footprint Program‏‎ (16:53, 31 January 2008)
  3. Example scripts‏‎ (17:00, 31 January 2008)
  4. INSPH‏‎ (18:10, 6 February 2008)
  5. Showsph.in‏‎ (18:15, 6 February 2008)
  6. Sequence alignment‏‎ (14:54, 8 February 2008)
  7. Flex.in‏‎ (17:17, 11 February 2008)
  8. 2008 Spring‏‎ (16:08, 20 February 2008)
  9. Grid.in‏‎ (16:53, 20 February 2008)
  10. BOSS Pure Liquid Simulation Notes‏‎ (14:56, 27 February 2008)
  11. Lab-designed code and programs‏‎ (15:11, 10 March 2008)
  12. Rename files in Unix‏‎ (15:11, 10 March 2008)
  13. Restraint04.pdb‏‎ (17:08, 28 March 2008)
  14. Restraint01.pdb‏‎ (17:09, 28 March 2008)
  15. 01mi.in‏‎ (17:14, 28 March 2008)
  16. 04md.in‏‎ (17:15, 28 March 2008)
  17. Disulfide.txt‏‎ (18:30, 28 March 2008)
  18. Config‏‎ (17:57, 4 April 2008)
  19. Visiting BNL‏‎ (16:44, 16 April 2008)
  20. Reference.vmd.script‏‎ (11:19, 21 April 2008)
  21. Restraint.vmd.script‏‎ (11:43, 21 April 2008)
  22. Setup ssh tunnel to NYBlue fen‏‎ (01:12, 24 April 2008)
  23. Vmd.rmsd.csh‏‎ (17:36, 11 May 2008)
  24. PDFCreator‏‎ (12:12, 12 May 2008)
  25. Making images for publication‏‎ (13:46, 12 May 2008)
  26. Using convert command unix‏‎ (14:30, 12 May 2008)
  27. Showbox.in‏‎ (16:29, 5 June 2008)
  28. Rigid.in‏‎ (16:30, 5 June 2008)
  29. Octave‏‎ (11:57, 11 June 2008)
  30. Histograms in R‏‎ (13:53, 11 June 2008)
  31. Apply for NYBlue‏‎ (10:45, 12 June 2008)
  32. Clustering in R‏‎ (15:37, 17 June 2008)
  33. Installing MSMS for VMD‏‎ (16:22, 23 June 2008)
  34. Gnuplot‏‎ (17:00, 14 July 2008)
  35. Make surface‏‎ (17:02, 14 July 2008)
  36. Ways to remove the first line‏‎ (11:19, 18 August 2008)
  37. Research Foundation‏‎ (11:11, 19 August 2008)
  38. Ptraj‏‎ (12:41, 20 August 2008)
  39. Get time estimate for free blocks‏‎ (15:18, 26 August 2008)
  40. Get time for job completion‏‎ (15:19, 26 August 2008)
  41. AMBER tricks‏‎ (15:25, 10 September 2008)
  42. 2007-2008 AMS-532 Fall-Spring‏‎ (17:38, 10 September 2008)
  43. Remove waters from trajectories‏‎ (08:26, 11 September 2008)
  44. 2006-2007 AMS-532 Fall-Spring‏‎ (13:22, 15 September 2008)
  45. X-Win32‏‎ (16:44, 13 January 2009)
  46. Submitting BlueGene Jobs‏‎ (14:22, 16 February 2009)
  47. Compiling Applications for BG/L‏‎ (14:31, 18 February 2009)
  48. Other Meetings‏‎ (13:11, 19 February 2009)
  49. Sampling Methods‏‎ (15:36, 23 February 2009)
  50. Families in the Protein Databank‏‎ (12:17, 25 February 2009)
  51. Common Errors - ctrl M‏‎ (12:37, 25 February 2009)
  52. Amber to pdb‏‎ (12:46, 25 February 2009)
  53. Pdb to mol2‏‎ (12:50, 25 February 2009)
  54. NAMD to mol2‏‎ (12:53, 25 February 2009)
  55. NAMD tutorial‏‎ (13:02, 4 May 2009)
  56. 2008-2009 AMS-532 Fall-Spring‏‎ (23:53, 10 May 2009)
  57. Ethernet Cables‏‎ (14:40, 12 June 2009)
  58. R - Statistical Computing‏‎ (18:50, 19 June 2009)
  59. NAMD Amber inputs‏‎ (12:43, 20 July 2009)
  60. Unix find‏‎ (22:38, 28 July 2009)
  61. Which Unix Distribution?‏‎ (16:36, 8 September 2009)
  62. Drug-like organic molecules‏‎ (21:34, 19 September 2009)
  63. Scp files from cluster to NYBlue‏‎ (14:56, 11 November 2009)
  64. Rotation students Wiki‏‎ (15:02, 8 December 2009)
  65. SDF to mol2‏‎ (12:46, 10 December 2009)
  66. No t4 step2 min.bash‏‎ (12:36, 18 January 2010)
  67. No t4 step2 equiprod.bash‏‎ (12:38, 18 January 2010)
  68. No t4 step3 inputgen.bash‏‎ (12:39, 18 January 2010)
  69. With t4 step1 inputgen.bash‏‎ (12:49, 18 January 2010)
  70. With t4 step2 min.bash‏‎ (12:50, 18 January 2010)
  71. With t4 step2 equiprod.bash‏‎ (12:53, 18 January 2010)
  72. With t4 step3 inputgen.bash‏‎ (12:54, 18 January 2010)
  73. Integration.pl‏‎ (16:08, 19 January 2010)
  74. TIMD integration.py‏‎ (16:10, 19 January 2010)
  75. TIMD integration prep.py‏‎ (16:15, 19 January 2010)
  76. TIMD extraction.py‏‎ (16:16, 19 January 2010)
  77. LoadLeveler Chain Jobs‏‎ (17:41, 25 January 2010)
  78. Amber to mol2 (protein)‏‎ (17:45, 25 January 2010)
  79. Sed - Stream Editor in Unix‏‎ (12:18, 1 February 2010)
  80. Get Job ids to use for llcancel‏‎ (14:09, 5 February 2010)
  81. Pylab‏‎ (15:03, 12 February 2010)
  82. Secure Shell (ssh)‏‎ (13:54, 1 March 2010)
  83. Optimize Polar Hydrogens‏‎ (20:57, 4 March 2010)
  84. Joint Group Meeting 2007-2009‏‎ (12:29, 7 April 2010)
  85. MPICH‏‎ (13:27, 14 April 2010)
  86. Amber on Seawulf (compilation)‏‎ (17:04, 19 April 2010)
  87. No t4 step1 inputgen.bash‏‎ (11:26, 2 June 2010)
  88. AMBER TI Tutorials‏‎ (17:50, 7 June 2010)
  89. Dell 5110cn Printer‏‎ (15:17, 1 July 2010)
  90. Sphere Generation‏‎ (20:34, 24 July 2010)
  91. AMS-532 Guidlines‏‎ (11:09, 28 July 2010)
  92. AMS-532: Lab Rotations/Journal Club Guidelines‏‎ (11:11, 28 July 2010)
  93. 2009-2010 AMS-532 Fall-Spring‏‎ (12:32, 12 August 2010)
  94. 2010 LAB‏‎ (14:31, 13 August 2010)
  95. Cluster compilations‏‎ (16:44, 15 September 2010)
  96. Making images for publication using vmd‏‎ (21:55, 12 October 2010)
  97. Joint Group Meeting 2010‏‎ (13:57, 19 October 2010)
  98. Archiving old data‏‎ (12:50, 29 November 2010)
  99. Past Announcements‏‎ (22:11, 9 December 2010)
  100. SB2011 testset‏‎ (10:53, 21 December 2010)
  101. Setting up RSA SecureID token‏‎ (17:40, 22 December 2010)
  102. 2009 AMBER tutorial with Trpcage‏‎ (11:01, 31 January 2011)
  103. 2008 AMBER tutorial‏‎ (11:01, 31 January 2011)
  104. 2009 DOCK tutorial with neuraminidase‏‎ (11:02, 31 January 2011)
  105. 2008 DOCK tutorial with 1LAH‏‎ (11:02, 31 January 2011)
  106. Blocked Standard Error of the Mean‏‎ (18:41, 7 February 2011)
  107. 2008-2009 LAB‏‎ (16:08, 23 March 2011)
  108. 2009 RCR GROUP MEETING‏‎ (16:21, 23 March 2011)
  109. 2008 RCR GROUP MEETING‏‎ (16:21, 23 March 2011)
  110. 2010 RCR GROUP MEETING‏‎ (16:21, 23 March 2011)
  111. 2011 AMBER Tutorial with Biotin and Streptavidin‏‎ (15:51, 25 March 2011)
  112. VMD‏‎ (08:41, 5 May 2011)
  113. Stupid awk tricks‏‎ (07:31, 6 May 2011)
  114. Fourier fit‏‎ (08:23, 6 May 2011)
  115. Valgrind‏‎ (17:22, 11 May 2011)
  116. 2008 DOCK tutorial with Gleevec‏‎ (10:30, 19 May 2011)
  117. Nonstandard residues prep‏‎ (21:40, 23 May 2011)
  118. Cancer‏‎ (14:31, 24 May 2011)
  119. Influenza‏‎ (14:32, 24 May 2011)
  120. HIV/AIDS‏‎ (14:52, 24 May 2011)
  121. MOE‏‎ (16:59, 15 July 2011)
  122. DOCK Compilation‏‎ (12:47, 18 July 2011)
  123. Genion.mdp‏‎ (15:12, 21 July 2011)
  124. Ubq min.mdp‏‎ (01:10, 22 July 2011)
  125. Ubq md.mdp‏‎ (12:36, 22 July 2011)
  126. Ubq nvt.mdp‏‎ (13:14, 22 July 2011)
  127. Ubq npt.mdp‏‎ (13:14, 22 July 2011)
  128. PBS Queue‏‎ (16:52, 25 July 2011)
  129. Method development‏‎ (09:39, 5 August 2011)
  130. Automated Families generation from the Protein Databank‏‎ (13:35, 12 August 2011)
  131. Ps.m2p‏‎ (11:11, 15 August 2011)
  132. Journal Articles from UCSF‏‎ (17:40, 27 October 2011)
  133. Joint Group Meeting 2012‏‎ (12:38, 15 November 2011)
  134. Joint Group Meeting 2011‏‎ (11:17, 8 December 2011)
  135. 2011 RCR GROUP MEETING‏‎ (12:11, 5 January 2012)
  136. Ghostscript‏‎ (09:19, 9 February 2012)
  137. Semester Checklist‏‎ (07:18, 10 February 2012)
  138. 2010 AMBER Tutorial with Biotin and Streptavidin‏‎ (10:22, 28 February 2012)
  139. MD Simulation: Protein in Water‏‎ (08:22, 29 February 2012)
  140. Stony Brook Joint Group Meetings in Computational Structural Biology‏‎ (12:03, 12 March 2012)
  141. Joint Group Meeting 2013‏‎ (12:04, 12 March 2012)
  142. 2009-2010 GRD-500 Fall-Spring‏‎ (09:32, 24 April 2012)
  143. 2010-2011 GRD-500 Fall-Spring‏‎ (09:34, 24 April 2012)
  144. 2011-2012 GRD-500 Fall-Spring‏‎ (09:35, 24 April 2012)
  145. 2010 GRD-500 Spring‏‎ (09:39, 24 April 2012)
  146. 2010 DOCK tutorial with Streptavidin‏‎ (18:54, 7 May 2012)
  147. 2011 DOCK tutorial with Streptavidin‏‎ (18:55, 7 May 2012)
  148. Virtual Screening Protocol on BlueGene (IGF-IR system)‏‎ (16:06, 25 July 2012)
  149. 2012 DOCK tutorial with Streptavidin‏‎ (12:22, 24 October 2012)
  150. Activating your Seawulf Account‏‎ (12:14, 19 November 2012)
  151. Formating your Thesis‏‎ (23:33, 9 January 2013)
  152. MATLAB‏‎ (18:51, 14 January 2013)
  153. MD Simulation: Protein in Water (Pt. 2)‏‎ (16:58, 15 January 2013)
  154. C Shell Scripting‏‎ (13:17, 30 January 2013)
  155. Rsync‏‎ (21:15, 18 February 2013)
  156. 2012 RCR GROUP MEETING‏‎ (19:27, 8 April 2013)
  157. Compiling GROMACS on Cluster‏‎ (15:59, 31 May 2013)
  158. Xmgrace‏‎ (14:57, 23 July 2013)
  159. AMS-532 Laboratory Rotations and Journal Club in Computational Biology‏‎ (15:18, 5 August 2013)
  160. 2010-2011 AMS-532 Fall-Spring‏‎ (15:22, 5 August 2013)
  161. GRD-500 Integrity in Science‏‎ (16:00, 5 August 2013)
  162. 2011 GRD-500 Spring‏‎ (16:00, 5 August 2013)
  163. 2012 GRD-500 Spring‏‎ (16:03, 5 August 2013)
  164. 2011-2012 AMS-532 Fall-Spring‏‎ (16:08, 5 August 2013)
  165. 2009 AMS-536 Spring‏‎ (17:22, 5 August 2013)
  166. 2010 AMS-536 Spring‏‎ (17:23, 5 August 2013)
  167. 2011 AMS-536 Spring‏‎ (17:23, 5 August 2013)
  168. 2012 AMS-536 Spring‏‎ (17:24, 5 August 2013)
  169. 2008 AMS-535 Fall‏‎ (09:52, 6 August 2013)
  170. 2009 AMS-535 Fall‏‎ (09:57, 6 August 2013)
  171. 2010 AMS-535 Fall‏‎ (09:59, 6 August 2013)
  172. 2011 AMS-535 Fall‏‎ (10:00, 6 August 2013)
  173. 2012 AMS-535 Fall‏‎ (10:03, 6 August 2013)
  174. 2013 AMS-536 Spring‏‎ (10:18, 7 August 2013)
  175. Wiki Editing‏‎ (17:12, 26 August 2013)
  176. Per-residue energy decompositions‏‎ (10:31, 17 September 2013)
  177. Coming Soon‏‎ (17:41, 19 November 2013)
  178. 2013 RCR GROUP MEETING‏‎ (17:06, 6 December 2013)
  179. 2012-2013 AMS-532 Fall-Spring‏‎ (17:11, 23 January 2014)
  180. Server Administration‏‎ (12:09, 7 March 2014)
  181. 2014 AMS-536 Spring‏‎ (15:18, 11 March 2014)
  182. 2012 AMBER Tutorial with Biotin and Streptavidin‏‎ (11:31, 26 March 2014)
  183. Announcements: Fall 2013‏‎ (10:27, 7 April 2014)
  184. 2013 AMS-535 Fall‏‎ (11:57, 7 April 2014)
  185. 2013-2014 AMS-532 Fall-Spring‏‎ (16:25, 9 April 2014)
  186. 2014 AMBER tutorial with HIV Protease‏‎ (21:14, 23 April 2014)
  187. AMBER Lipid Tutorials‏‎ (13:36, 25 August 2014)
  188. 2014 DOCK tutorial with HIV Protease‏‎ (18:05, 17 December 2014)
  189. 2014 RCR GROUP MEETING‏‎ (12:31, 22 December 2014)
  190. 2013 AMBER Tutorial with UMP and OMP‏‎ (16:54, 6 January 2015)
  191. 2013 DOCK tutorial with Orotodine Monophosphate Decarboxylase‏‎ (17:26, 14 January 2015)
  192. Energy Scoring Method in Grid‏‎ (14:24, 5 March 2015)
  193. NAMD on Seawulf‏‎ (23:51, 6 March 2015)
  194. 2014-2015 AMS-532 Fall-Spring‏‎ (08:36, 25 March 2015)
  195. 2015 DOCK tutorial with Poly(ADP-ribose) polymerase (PARP)‏‎ (14:16, 25 March 2015)
  196. Getting a BNL Account‏‎ (11:28, 1 May 2015)
  197. Apply for cluster‏‎ (13:53, 1 May 2015)
  198. 2015 AMS-536 Spring‏‎ (14:55, 4 May 2015)
  199. CVS Commands‏‎ (20:02, 10 August 2015)
  200. DOCK Benchmarking‏‎ (03:15, 12 November 2015)
  201. 2015 RCR GROUP MEETING‏‎ (10:44, 10 December 2015)
  202. 2016 AMBER tutorial with Thrombin‏‎ (14:16, 6 April 2016)
  203. 2016 AMBER tutorial with Beta Trypsin‏‎ (14:51, 12 May 2016)
  204. 2008 AMS-536 Spring‏‎ (12:44, 1 June 2016)
  205. 2016 RCR GROUP MEETING‏‎ (11:14, 10 August 2016)
  206. 2015-2016 AMS-532 Fall-Spring‏‎ (15:47, 10 August 2016)
  207. 2015 AMS-535 Fall‏‎ (12:42, 12 August 2016)
  208. Seawulf Programs Needed‏‎ (21:21, 12 October 2016)
  209. Seawulf Cluster Assessment‏‎ (15:09, 19 October 2016)
  210. ZINC Database‏‎ (11:18, 27 October 2016)
  211. ZINC12 Database‏‎ (11:28, 27 October 2016)
  212. ZINC15 Database‏‎ (18:08, 22 November 2016)
  213. DOCK Denovo Run‏‎ (16:34, 30 November 2016)
  214. 2016 AMS-535 Fall‏‎ (14:23, 8 December 2016)
  215. DOCK Denovo Refinement‏‎ (14:15, 18 January 2017)
  216. 2016 DOCK tutorial with Beta Trypsin‏‎ (17:53, 30 January 2017)
  217. 2018‏‎ (17:47, 1 February 2017)
  218. 2017 Dock tutorial‏‎ (17:47, 1 February 2017)
  219. 2017a DOCK tutorial‏‎ (16:56, 6 February 2017)
  220. 2017 DOCK tutorial 2 with PDB 3GPL NEW‏‎ (17:59, 8 March 2017)
  221. 2017 DOCK tutorial 1 with PDB 4QMZ NEW‏‎ (18:10, 8 March 2017)
  222. Seawulf Items Needed‏‎ (14:36, 9 March 2017)
  223. 2017 Denovo design tutorial with PDB 1BJU‏‎ (17:09, 22 March 2017)
  224. 2017 AMS-536 Spring‏‎ (16:21, 10 April 2017)
  225. RGD‏‎ (12:34, 28 April 2017)
  226. Joe and Brian de novo stuff‏‎ (13:37, 20 June 2017)
  227. 2017 AMBER tutorial with 4qmz‏‎ (12:18, 5 July 2017)
  228. 2016-2017 AMS-532 Fall-Spring‏‎ (10:28, 11 July 2017)
  229. DOCK Denovo‏‎ (12:36, 3 October 2017)
  230. 2017 RCR GROUP MEETING‏‎ (14:28, 19 December 2017)
  231. De novo DOCK‏‎ (13:44, 17 January 2018)
  232. CONGA‏‎ (10:57, 29 January 2018)
  233. DOCK NOVA‏‎ (14:52, 16 February 2018)
  234. NOVA‏‎ (14:55, 16 February 2018)
  235. CONGA (CONstruction by Genetic Algorithm)‏‎ (14:59, 16 February 2018)
  236. Fragment Library Generation‏‎ (16:00, 19 February 2018)
  237. 2018 AMS-536 Spring‏‎ (15:24, 26 March 2018)
  238. 2018 AMBER tutorial with 1c87‏‎ (16:26, 4 April 2018)
  239. De novo Benchmarking‏‎ (09:54, 26 April 2018)
  240. 3D Analog Library Generation Using Pubchem and Zinc‏‎ (10:36, 22 May 2018)
  241. 2018 RCR GROUP MEETING‏‎ (13:48, 9 July 2018)
  242. NOVA (Navigation and Optimization for Virtual Assembly)‏‎ (12:13, 25 July 2018)
  243. 2017-2018 AMS-532 Fall-Spring‏‎ (11:12, 25 August 2018)
  244. CONGA Parameter List‏‎ (15:11, 28 August 2018)
  245. Example of an Input file‏‎ (14:46, 6 September 2018)
  246. De Novo Design (previously NOVA)‏‎ (16:27, 6 September 2018)
  247. Make Unique script usage‏‎ (16:35, 6 September 2018)
  248. Footprint Plot Visualization‏‎ (12:14, 7 September 2018)
  249. Example of an CONGA Input file‏‎ (11:27, 10 September 2018)
  250. De Novo Design‏‎ (11:30, 10 September 2018)

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