March 2015 *********** 1) regular meeting time 3:30 Tuesday 2) sign up for bluewaters email me your text March 20 is deadline 3) time sheets anik 4) modeling status of histone/DNA complex /autotmb/simulations/MonoNucs/utils see P-fit-pos.vmd and fit-pro-to-chrom.vmd idea once have fixed the histones is to a)align "fixed" histones to histones in the xray using whatever backbone atoms we can b)align "folded" dna (see ICM for making a folded DNA) to the xray using phosphates c) save the fitted histone and the folded DNA d) rebuild structure w/ amber e) solvate/add ions/ minimize/eq NOTES: anik havin'g libreoffice and firefox issues March 24 2015 ****************** fixing the x-ray structures with SwissPDB view/modeller 1) getting spdb to work a) run winecfg this makes a ~/.wine file b) unzip /usr/local/src/MoleModeling/SwissPDB/SPDBV_4.10_PC.zip in cd "~/.wine/drive_c/Program Files" cp /usr/local/src/MoleModeling/SwissPDB/SPDBV_4.10_PC.zip . gunzip SPDBV_4.10_PC.zip c) start SwissPDB wine ~/.wine/drive_c/Program\ Files/SPDBV_4.10_PC/spdbv.exe d) make this a ~/.alias so you never have to do it again vi ~/.alias and add the following alias spdb 'wine ~/.wine/drive_c/Program\ Files/SPDBV_4.10_PC/spdbv.exe' 2) now on to the work at hand cp 1kx5 and 2cv5 to some directory now we'll clean them up 1KX5: this is xenopus! do point mutations to change the points on 1kx5:[D,H] Residue 33 is actually already Serine so what's PDB reporting? do this w/ spdb's mutate button/home/bishop/public_html/Lab/Notes//2015/Mar2015.txt 1kx5:[C,G] change Residue 100 to Gly (local seq is LLGGVT) and Residue 124 to Ala local sequence is (ESAKS) do this w/ spdb's mutate button 1kx5:[A,E] Residue 103 is supposed to be Gly local sequence is LVGLF so do this mutation w/ spdb's mutate button 1kx5:[C,G] there is a missing Ala at position 127 so break the backbone between S 126 and K 127 and insert the missing A then ligate the backbone select use the molecular mechanics and select only this region to minimize /home/bishop/public_html/Lab/Notes//2015/Mar2015.txt and quickly fix it NOW TE HEAVY LIFTING: 1kx5:[D,H] add the missing MPEP to the N term s.t. it's MPEPAKSAP you can assign any secondary structure yodu like to this just add the MPEP to the end in reverse order PEPM onto the Alanine finally I'd like to straighten out the tail of chain A so it matches that of chain E some what extended should be OK so extract the 2ndary structure map from chain E from about Valine 35 to the end and use the threading tools of Swisspdb to enforce the s.s. of E onto A that should be all there is to fix up 1kx5 we now have a complete xenopus 1xk5 2) 1kx5 MOUSE we shold be able to thread the mouse sequence onto 1kx5 using swisspdb one chain at a time shold work... 3) 1kx5 human/home/bishop/public_html/Lab/Notes//2015/Mar2015.txt likewise we should be able to thread human sequence onto 1kx5 using swisspdb NOW ON TO FIXING 2CV5 1) all chains in 2CV5 are incomplete H3.1 A,E are missing 1-38(39 chnA) and chnA is missing 135 H4 B,F are missing 1-18 and 1-25 (F,B) H2A.a C,G missing 1-11 nad 1-15 respectively and on C term both are missing 118 to 130 H2B D,H missing 1-30 and 1-31 respectivey and H is missing 126 the idea will be to take all of these missing parts from our 1KX5 that we have mutated to human and create a complete 2cv5 human model 2) once have complete 2cv5 human then thread thru the xenopus and mouse sequences ****************************** March 31, 2015 1) completed models of frog,human and mouse nucleosome based on 1KX5 and 2CV5 have been made see gua 105% ls /simulations/MonoNucs/1KX5/ frog/ human/ in/ mod/ mouse/ gua 106% ls /simulations/MonoNucs/2CV5/ frog/ human/ in/ mod/ mouse/ TODO: Anik: human Ran: mouse Bishop: frog 0) check that sequence is same in each AND that is corrrect as per PDB/entrez entries 1) check that structure is "correct" can use spdb to "magic" fit to x-ray and should get a very low < 1A RMSD answer 2) run a simple namd minimization of the vacuum system and see what happens need to determine a) does it run b) does anything pathological happen, view it w/ VMD to find out c) single plot of bond,angle,dihedral energies ... all should converge ~1000 steps d) separate plots of elec, vdw, and PE should also converg about ~1000 steps e) check other energies to see what is happending f) make plot of rmsd and determmine how long for rms to converge 3) do a test run in fac. w/ equilibration beginning from the minimized structure a) does running w/out minimization work? b) any thing pathological? c) how long for temperature to equilibrate to 300K? 4) DOING IT RIGHT: 1) check the ABC 2014 paper and find out what cut-off and other parameters were used find the NAMD equivalent and consider their heating protocol GOAL: is a proper namd eq1.conf file that does heating and has proper parameters OTHER: 1) help sandeep get started 2) time sheets and calendars filled in 3) meeting/progress during the week... we need to meet more often now that have structures 4) BlueWaters 5) data and file management ideas: tmbshare web holds group-policy tips-tricks software and howtos getting-started contact information Talks and TODO: bishop sets up template for web files they fill them in 6) April 15