Setup_of_a_Molecularinitial_structure00 crystal ​structure​ of the protein 2016-06-16 13:07:02.425 UTC build/structure.pdb 2016-06-16 13:46:46.624 UTC topology_prot00 toppar/top_all22_prot.rtf 2016-06-16 13:46:53.859 UTC topology file for protein​s 2016-06-16 13:46:12.942 UTC topology_carb00 topology file for carbohydrates 2016-06-16 13:47:05.354 UTC toppar/top_all36_carb.rtf 2016-06-16 13:47:08.58 UTC topology_pca00 topology file for ​the non-standard residue PCA 2016-06-16 13:47:18.698 UTC toppar/pca.rtf 2016-06-16 13:47:22.27 UTC final_structure_20final_structure_10 coordinates for the whole system (cbh1.pdb), indicating which atoms should be kept fixed along the simulation​ 2016-06-16 13:41:39.621 UTC splitinitial_structure0protein_pdb00bglc_pdb00cal_pdb00water_pdb00 the file structure.pdb is split into different parts. Each part represent a subsystem.​ 2016-06-16 13:15:17.844 UTC net.sf.taverna.t2.activitiesexternal-tool-activity1.5net.sf.taverna.t2.activities.externaltool.ExternalToolActivity 789663B8-DA91-428A-9F7D-B3F3DA185FD4 default local <?xml version="1.0" encoding="UTF-8"?> <localInvocation><shellPrefix>/bin/sh -c</shellPrefix><linkCommand>/bin/ln -s %%PATH_TO_ORIGINAL%% %%TARGET_NAME%%</linkCommand></localInvocation> 3f0be5d7-37b8-4f28-a1a2-d2fe2fdb7d30 grep ATOM structure.pdb > protein.pdb grep HOH structure.pdb > water.pdb grep GLC structure.pdb > bglc.pdb grep CAL structure.pdb > cal.pdb 1200 1800 initial_structure structure.pdb true false false UTF-8 false false false cal_pdb cal.pdb false protein_pdb protein.pdb false water_pdb water.pdb false bglc_pdb bglc.pdb false true true true 0 false net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokepsgentopology_pca0topology_carb0topology_prot0protein_pdb0bglc_pdb0cal_pdb0water_pdb0hyd_pdb00hyd_psf00 Starting the program psfgen​. This program takes the 4 files above, and assign force field parameters (charges, bonds etc) for the system. 2016-06-16 13:20:55.653 UTC net.sf.taverna.t2.activitiesexternal-tool-activity1.5net.sf.taverna.t2.activities.externaltool.ExternalToolActivity 789663B8-DA91-428A-9F7D-B3F3DA185FD4 default local <?xml version="1.0" encoding="UTF-8"?> <localInvocation><shellPrefix>/bin/sh -c</shellPrefix><linkCommand>/bin/ln -s %%PATH_TO_ORIGINAL%% %%TARGET_NAME%%</linkCommand></localInvocation> fec2a5a0-ae3c-4981-bfae-087a065acf17 /home/lucas/programas/namd/psfgen << ENDMOL # Read topology file topology top_all22_prot.rtf topology pca.rtf topology top_all36_carb.rtf # Build protein segment pdbalias atom ILE CD1 CD pdbalias residue HIS HSP segment CBH1 { first none pdb protein.pdb mutate 251 ALA } patch GLUP CBH1:119 patch ASPP CBH1:214 patch GLUP CBH1:217 patch GLUP CBH1:223 patch GLUP CBH1:334 patch ASPP CBH1:368 patch ASPP CBH1:378 patch DISU CBH1:138 CBH1:397 patch DISU CBH1:261 CBH1:331 patch DISU CBH1:25 CBH1:19 patch DISU CBH1:172 CBH1:210 patch DISU CBH1:230 CBH1:256 patch DISU CBH1:176 CBH1:209 patch DISU CBH1:238 CBH1:243 patch DISU CBH1:4 CBH1:72 patch DISU CBH1:67 CBH1:61 patch DISU CBH1:50 CBH1:71 regenerate angles dihedrals coordpdb protein.pdb CBH1 # Build carbohydrate segment pdbalias residue GLC BGLC segment BGLC { pdb bglc.pdb } patch 14bb BGLC:452 BGLC:453 patch 14bb BGLC:453 BGLC:454 patch 14bb BGLC:454 BGLC:455 patch 14bb BGLC:455 BGLC:456 patch 14bb BGLC:456 BGLC:457 patch 14bb BGLC:457 BGLC:458 patch 14bb BGLC:458 BGLC:459 patch 14bb BGLC:459 BGLC:460 regenerate angles dihedrals coordpdb bglc.pdb BGLC # Build structural waters segment pdbalias residue HOH TIP3 pdbalias atom HOH O OH2 segment H2O { auto none pdb water.pdb} coordpdb water.pdb H2O # Build Calcium segment segment CAL { pdb cal.pdb } coordpdb cal.pdb CAL # Guess missing coordinates guesscoord # Write structure and coordinate files writepdb hyd.pdb writepsf hyd.psf ENDMOL rm protein.pdb water.pdb bglc.pdb cal.pdb 1200 1800 topology_pca pca.rtf true false false UTF-8 false false false topology_carb top_all36_carb.rtf true false false UTF-8 false false false topology_prot top_all22_prot.rtf true false false UTF-8 false false false cal_pdb cal.pdb true false false UTF-8 false false false protein_pdb protein.pdb true false false UTF-8 false false false water_pdb water.pdb true false false UTF-8 false false false bglc_pdb bglc.pdb true false false UTF-8 false false false hyd_pdb hyd.pdb false hyd_psf hyd.psf false true true true 0 false net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokesolvatehyd_pdb0hyd_psf0wbox_pdb00wbox_psf00 Using the program solvate​ ​to imerse the system in a water box.​ 2016-06-16 13:31:43.53 UTC net.sf.taverna.t2.activitiesexternal-tool-activity1.5net.sf.taverna.t2.activities.externaltool.ExternalToolActivity 789663B8-DA91-428A-9F7D-B3F3DA185FD4 default local <?xml version="1.0" encoding="UTF-8"?> <localInvocation><shellPrefix>/bin/sh -c</shellPrefix><linkCommand>/bin/ln -s %%PATH_TO_ORIGINAL%% %%TARGET_NAME%%</linkCommand></localInvocation> 6638ca10-c81d-475d-ae5b-2ee2cb30cd3c echo " package require solvate solvate hyd.psf hyd.pdb -rotate -t 16 -o wbox exit " > solv.tcl vmd -dispdev text -e solv.tcl rm solv.tcl 1200 1800 hyd_pdb hyd.pdb true false false UTF-8 false false false hyd_psf hyd.psf true false false UTF-8 false false false wbox_pdb wbox.pdb false wbox_psf wbox.psf false true true true 0 false net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeionizewbox_pdb0wbox_psf0cbh1_pdb00cbh1_psf00 With the program autoionize, introduce ions to neutralize the system.​ 2016-06-16 13:32:02.874 UTC net.sf.taverna.t2.activitiesexternal-tool-activity1.5net.sf.taverna.t2.activities.externaltool.ExternalToolActivity 789663B8-DA91-428A-9F7D-B3F3DA185FD4 default local <?xml version="1.0" encoding="UTF-8"?> <localInvocation><shellPrefix>/bin/sh -c</shellPrefix><linkCommand>/bin/ln -s %%PATH_TO_ORIGINAL%% %%TARGET_NAME%%</linkCommand></localInvocation> 25b68d06-2010-4e6e-a915-45f2f77f593e # ionic strength = 0.10 echo " package require autoionize autoionize -psf wbox.psf -pdb wbox.pdb -nna 21 -ncl 10 -o cbh1 exit " > ionize.tcl vmd -dispdev text -e ionize.tcl #rm ionize.tcl wbox* hyd* 1200 1800 wbox_pdb wbox.pdb true false false UTF-8 false false false wbox_psf wbox.psf true false false UTF-8 false false false cbh1_pdb cbh1.pdb false cbh1_psf cbh1.psf false true true true 0 false net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokeconstraints_definitioncbh1_pdb0cbh1_psf0fixed_1_pdb00fixed_2_pdb00 We define the atoms that should be kept fixed in the equilibration steps of the MD simulations.​ 2016-06-16 13:32:53.322 UTC net.sf.taverna.t2.activitiesexternal-tool-activity1.5net.sf.taverna.t2.activities.externaltool.ExternalToolActivity 789663B8-DA91-428A-9F7D-B3F3DA185FD4 default local <?xml version="1.0" encoding="UTF-8"?> <localInvocation><shellPrefix>/bin/sh -c</shellPrefix><linkCommand>/bin/ln -s %%PATH_TO_ORIGINAL%% %%TARGET_NAME%%</linkCommand></localInvocation> 2eebba80-cb4b-4574-9ee2-b1fb3850f0fd echo ' mol new cbh1.psf mol addfile cbh1.pdb set all [atomselect top all] $all set beta 0 set fixed [atomselect top "(protein or segname BGLC) and noh"] $fixed set beta 500 $all writepdb fixed.1.pdb set all [atomselect top all] $all set beta 0 set fixed [atomselect top "protein and name CA"] $fixed set beta 500 $all writepdb fixed.2.pdb exit ' > fixed.tcl vmd -dispdev text -e fixed.tcl rm fixed.tcl 1200 1800 cbh1_pdb cbh1.pdb true false false UTF-8 false false false cbh1_psf cbh1_psf true false false UTF-8 false false false fixed_2_pdb fixed.2.pdb false fixed_1_pdb fixed.1.pdb false false true true 0 false net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Parallelize 1 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.ErrorBouncenet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Failovernet.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Retry 1.0 1000 5000 0 net.sf.taverna.t2.coreworkflowmodel-impl1.5net.sf.taverna.t2.workflowmodel.processor.dispatch.layers.Invokesplitinitial_structureinitial_structurepsgentopology_pcatopology_pcapsgentopology_carbtopology_carbpsgentopology_prottopology_protpsgenprotein_pdbsplitprotein_pdbpsgenbglc_pdbsplitbglc_pdbpsgencal_pdbsplitcal_pdbpsgenwater_pdbsplitwater_pdbsolvatehyd_pdbpsgenhyd_pdbsolvatehyd_psfpsgenhyd_psfionizewbox_pdbsolvatewbox_pdbionizewbox_psfsolvatewbox_psfconstraints_definitioncbh1_pdbionizecbh1_pdbconstraints_definitioncbh1_psfionizecbh1_psffinal_structure_2constraints_definitionfixed_2_pdbfinal_structure_1constraints_definitionfixed_1_pdb 97ab3da7-e068-4329-876d-643713ecd0fe 2015-04-14 20:27:27.81 UTC e2e01c59-a372-4380-87c6-4c76a6e22779 2015-04-14 17:44:04.216 UTC 94694d73-8418-4993-8e69-8451b7205c41 2015-04-14 21:06:46.33 UTC 805d0525-899f-4bcf-86fa-6127f4f0b016 2015-04-14 18:11:06.549 UTC 59328f6b-9698-4449-b8a4-65d56181d20e 2015-04-14 19:04:53.207 UTC 0b7602a4-0a05-4b33-8cf3-44eca9abc003 2015-03-26 17:00:04.280 UTC 88f71f4e-6770-405a-9b36-fd26640bfab5 2015-11-06 20:42:58.599 UTC 4e0806b9-3cf9-4030-9e8a-5108a6259277 2016-06-16 13:59:37.869 UTC 6247d992-85f8-4d7c-8454-9d4004084fb4 2015-11-06 20:40:54.278 UTC b118212d-e65d-4906-b986-8c7d6aa24c7b 2015-04-14 17:42:43.930 UTC ac131908-8826-4573-a48a-8ac969f235d4 2015-03-24 17:58:20.888 UTC 8cbe526d-4b96-4425-93be-a06c1ecbad66 2015-11-09 11:25:01.152 UTC cef2f2ff-a7c4-41a5-9b18-a59a012e374c 2015-11-06 20:37:20.551 UTC 32626c21-da0e-4aeb-ac93-8727122a1293 2016-06-16 14:25:05.791 UTC 270eb64e-d701-464c-9867-f99c94ab38ad 2016-06-16 13:49:50.697 UTC 42540f55-c669-4438-b092-6e5ea6466c3d 2015-04-14 20:47:28.220 UTC 66c7f223-3a65-4f33-8d33-762ea9dd86c7 2015-11-06 11:34:23.772 UTC 3fd44fad-fa57-4d1e-8592-725f872fce54 2015-03-24 18:21:02.854 UTC c1413f90-1545-4607-8054-0eb4c733eedd 2015-04-14 17:57:00.671 UTC 193e0018-9ad1-49fa-a7cd-8ababc58cbc4 2015-11-06 20:44:50.727 UTC d009da0f-d644-4a62-9b0f-9c0ce1fdbbf2 2015-11-06 20:38:29.461 UTC 424e5444-0300-4c2a-8b23-047412fd4375 2015-11-06 20:36:52.727 UTC 7ee117ba-3d9d-4f65-905a-68e95246fc0b 2015-11-06 11:55:25.864 UTC e73e8c08-61ef-4eff-af1e-14a58f8ad1b8 2015-04-14 17:41:15.204 UTC This script is used to build initial structures for a MD simulation of a protein in water, containing a glucan chain and ions​ 2016-06-16 13:09:01.953 UTC ac0df93c-a81c-4530-b93d-5bb1c3b34be2 2015-11-06 17:36:51.665 UTC Setup of a Molecular Dynamics Simulation 2015-11-06 11:18:10.968 UTC 3502e4fb-483e-4697-b41e-b8f966eee8b5 2015-04-14 18:02:06.431 UTC 32c9d4cc-4e63-4ddf-b2c8-d2a1279613d7 2015-11-06 14:28:03.427 UTC 6df5d80b-4386-4056-9ca3-ae17f7b0578d 2016-05-30 18:08:15.673 UTC d52ad52e-6066-4cb3-b985-354286780b50 2015-03-24 17:54:53.985 UTC f9ce81c6-a3c5-465e-8957-b3e2c5fdde41 2015-04-14 17:46:29.304 UTC 73c8521a-7c1a-4e9a-ae90-57f05e0168b2 2015-04-14 18:21:21.451 UTC 43389585-ccee-404d-8d32-d7d409e305e5 2015-11-06 19:22:59.440 UTC 2f5540d9-13ee-483b-bbfd-b2c4852d4c80 2015-11-06 17:34:21.584 UTC bede3dc7-d421-4553-bc0f-6880e2ca6da9 2015-04-14 17:47:48.596 UTC d8bd7e80-c2cf-47b4-b709-f7ae30d05166 2015-11-06 14:37:45.966 UTC 62dd80fb-d16e-4c55-9888-252fd6a4d5ba 2015-04-14 18:09:35.640 UTC 5adf48ed-0cea-4d67-ba23-f098d4fc8e88 2015-04-14 20:21:30.455 UTC e7fe8708-ee31-40a0-9b44-c56c7800d329 2015-11-06 11:31:14.23 UTC 2eb05842-29c4-407f-9713-9e68c582b8c5 2015-04-14 17:45:30.803 UTC Workflow's author: Lucas Carvalho Script's Author: Rodrigo Slveira Acknoledgments: Caroline Simões and Munir Skaf 2016-06-16 13:08:41.665 UTC 5b30e0e9-93e9-4240-9930-2ccf3f89b273 2015-11-06 11:52:50.904 UTC ca5d5c51-4dc2-4a67-a244-c4a3bb2de1e8 2015-11-06 20:38:02.575 UTC fc3ee5e5-b469-4690-9e93-a6f679a5a013 2015-04-14 18:03:42.143 UTC 89aeff34-6f84-4193-816e-001dd6659f4f 2015-10-08 19:26:35.23 UTC 31ef60dc-99e6-4c1b-bc82-d37bf7f0e07f 2016-05-30 16:53:32.111 UTC 0ec7e8c9-87c0-485c-9891-12cf0eea9ddc 2015-04-14 20:43:15.393 UTC 429e40c3-39ab-45c3-a90e-047ee2875b45 2015-04-14 20:48:34.102 UTC 983a8732-b199-45f1-a081-7162d23cfe9a 2016-06-16 13:58:04.979 UTC b83a6b33-1077-4791-a55a-4041ad679639 2015-11-06 14:32:30.823 UTC fcd42daf-079c-474b-9397-7e573bdc3bb8 2015-04-14 20:31:42.999 UTC 765fce4b-6372-4cf8-9e03-7d52bef9b383 2015-04-14 20:50:48.587 UTC 1d1f1788-756f-4531-ba4a-f4827a7a0f92 2015-04-14 18:58:21.185 UTC 067d2723-e91d-4835-ac99-e3f80f27587a 2015-04-14 20:20:23.833 UTC 8dbf86c6-cc60-46a6-85d8-36d5236dea7c 2015-04-14 17:35:15.845 UTC 73394599-a435-4178-9a8e-b0bdb9ede8a0 2015-04-14 21:05:39.140 UTC e10a2823-3f0e-41bc-8c60-38f6068c5fa3 2016-05-30 18:24:33.924 UTC 18d7b0e3-03c7-46bb-b0ad-5b5d9e9f8797 2015-03-24 18:03:20.121 UTC 273a2097-9a96-4e71-a8c6-b7304717fbe8 2015-04-14 19:06:45.407 UTC cd70aede-3a05-4148-a507-3ef19fa568b1 2016-06-16 13:51:25.706 UTC e888a2e3-dfba-46d2-9f02-daefa1a800fc 2015-11-06 11:32:15.565 UTC 69d9af58-95e7-4a07-8eb9-658856b40b9b 2015-04-14 18:11:54.138 UTC