Finished Rough tutorial

README.md

@@ -39,7 +39,42 @@ Select Tools > View In PyMOL > Workspace. Remove hydrogens on all protein and li
 
 ![HydroRemove](/images/removeHydrogens.png)
 
-
-
-
-
+**Save the PDB as desmondOut.pdb, This is important for the script below to run automatically!**
+
+##Step 5: reformat PDB
+Copy POPC.csv, found in the includes folder, to the working folder and run the following terminal commands:
+
+```
+awk '{if ($4 == "SPC") printf("%4s %6d %-4s %-4s %5d %10.3f %7.3f %7.3f  1.00  0.00\n"), $1, $2, $3, $4, $5,$6,$7,$8; else print $0}' desmondOut.pdb > SPCfix.pdb
+sed 's/SPC/WAT/' SPCfix.pdb > WATfix.pdb
+awk '{if ($4 == "ACE" && $3 != "C") next; else print $0}' WATfix.pdb > ACEfix.pdb
+awk '{if ($4 == "NMA" && $3 != "N") next; else print $0}'  ACEfix.pdb | sed 's/NMA/NME/' > NMEfix.pdb
+charmmlipid2amber.py -c POPC.csv -i NMEfix.pdb -o LipidFix.pdb
+sed 's/CL/Cl-/' LipidFix.pdb | sed 's/NA/Na+/' | sed 's/  CL/Cl-/' | sed 's/  NA/Na+/' > SaltFix.pdb
+awk '/NME/{print $0 ;print "Ter";next}1' SaltFix.pdb > TerFIX.pdb
+```
+Next, open TerFIX.pdb and add CYX residues, if applicaplbe, and renumber NME residues by +1 (NME A 348A -> NME A 349)
+
+![Renumb](/images/terminal.png)
+
+##Step 6: TLeap input
+Extract the box dimensions from *desmond_setup_1-out.cms* 
+
+```
+  69.378655
+  0
+  0
+  0
+  64.033248
+  0
+  0
+  0
+  95.385489
+
+```
+
+To set TLeap system dimensions add the following line in your leap.in:
+
+`
+set YOUR_NAME_HERE box { 69.378655 64.033248 95.385489}
+`

example/POPC.csv

@@ -0,0 +1,136 @@
+charmmlipid.csv Version 2.0.1
+residue,order,search,replace,TER,num_atom
+POPC,0, C32 POPC, C12 PA  ,True,134
+POPC,1, H2X POPC, H2R PA  ,True,134
+POPC,2, H2Y POPC, H2S PA  ,True,134
+POPC,3, C33 POPC, C13 PA  ,True,134
+POPC,4, H3X POPC, H3R PA  ,True,134
+POPC,5, H3Y POPC, H3S PA  ,True,134
+POPC,6, C34 POPC, C14 PA  ,True,134
+POPC,7, H4X POPC, H4R PA  ,True,134
+POPC,8, H4Y POPC, H4S PA  ,True,134
+POPC,9, C35 POPC, C15 PA  ,True,134
+POPC,10, H5X POPC, H5R PA  ,True,134
+POPC,11, H5Y POPC, H5S PA  ,True,134
+POPC,12, C36 POPC, C16 PA  ,True,134
+POPC,13, H6X POPC, H6R PA  ,True,134
+POPC,14, H6Y POPC, H6S PA  ,True,134
+POPC,15, C37 POPC, C17 PA  ,True,134
+POPC,16, H7X POPC, H7R PA  ,True,134
+POPC,17, H7Y POPC, H7S PA  ,True,134
+POPC,18, C38 POPC, C18 PA  ,True,134
+POPC,19, H8X POPC, H8R PA  ,True,134
+POPC,20, H8Y POPC, H8S PA  ,True,134
+POPC,21, C39 POPC, C19 PA  ,True,134
+POPC,22, H9X POPC, H9R PA  ,True,134
+POPC,23, H9Y POPC, H9S PA  ,True,134
+POPC,24,C310 POPC,C110 PA  ,True,134
+POPC,25,H10X POPC,H10R PA  ,True,134
+POPC,26,H10Y POPC,H10S PA  ,True,134
+POPC,27,C311 POPC,C111 PA  ,True,134
+POPC,28,H11X POPC,H11R PA  ,True,134
+POPC,29,H11Y POPC,H11S PA  ,True,134
+POPC,30,C312 POPC,C112 PA  ,True,134
+POPC,31,H12X POPC,H12R PA  ,True,134
+POPC,32,H12Y POPC,H12S PA  ,True,134
+POPC,33,C313 POPC,C113 PA  ,True,134
+POPC,34,H13X POPC,H13R PA  ,True,134
+POPC,35,H13Y POPC,H13S PA  ,True,134
+POPC,36,C314 POPC,C114 PA  ,True,134
+POPC,37,H14X POPC,H14R PA  ,True,134
+POPC,38,H14Y POPC,H14S PA  ,True,134
+POPC,39,C315 POPC,C115 PA  ,True,134
+POPC,40,H15X POPC,H15R PA  ,True,134
+POPC,41,H15Y POPC,H15S PA  ,True,134
+POPC,42,C316 POPC,C116 PA  ,True,134
+POPC,43,H16X POPC,H16R PA  ,True,134
+POPC,44,H16Y POPC,H16S PA  ,True,134
+POPC,45,H16Z POPC,H16T PA  ,True,134
+POPC,46, N   POPC, N31 PC  ,True,134
+POPC,47, C11 POPC, C32 PC  ,True,134
+POPC,48, H11 POPC, H2A PC  ,True,134
+POPC,49, H12 POPC, H2B PC  ,True,134
+POPC,50, C12 POPC, C33 PC  ,True,134
+POPC,51, H21 POPC, H3A PC  ,True,134
+POPC,52, H22 POPC, H3B PC  ,True,134
+POPC,53, H23 POPC, H3C PC  ,True,134
+POPC,54, C14 POPC, C34 PC  ,True,134
+POPC,55, H41 POPC, H4A PC  ,True,134
+POPC,56, H42 POPC, H4B PC  ,True,134
+POPC,57, H43 POPC, H4C PC  ,True,134
+POPC,58, C13 POPC, C35 PC  ,True,134
+POPC,59, H31 POPC, H5A PC  ,True,134
+POPC,60, H32 POPC, H5B PC  ,True,134
+POPC,61, H33 POPC, H5C PC  ,True,134
+POPC,62, C15 POPC, C31 PC  ,True,134
+POPC,63, H51 POPC, H1A PC  ,True,134
+POPC,64, H52 POPC, H1B PC  ,True,134
+POPC,65, P1  POPC, P31 PC  ,True,134
+POPC,66, O3  POPC, O33 PC  ,True,134
+POPC,67, O4  POPC, O34 PC  ,True,134
+POPC,68, O1  POPC, O32 PC  ,True,134
+POPC,69, O2  POPC, O31 PC  ,True,134
+POPC,70, C1  POPC, C3  PC  ,True,134
+POPC,71, HA  POPC, HA  PC  ,True,134
+POPC,72, HB  POPC, HB  PC  ,True,134
+POPC,73, C2  POPC, C2  PC  ,True,134
+POPC,74, HS  POPC, HX  PC  ,True,134
+POPC,75, O21 POPC, O21 PC  ,True,134
+POPC,76, C21 POPC, C21 PC  ,True,134
+POPC,77, O22 POPC, O22 PC  ,True,134
+POPC,78, C3  POPC, C1  PC  ,True,134
+POPC,79, HX  POPC, HR  PC  ,True,134
+POPC,80, HY  POPC, HS  PC  ,True,134
+POPC,81, O31 POPC, O11 PC  ,True,134
+POPC,82, C31 POPC, C11 PC  ,True,134
+POPC,83, O32 POPC, O12 PC  ,True,134
+POPC,84, C22 POPC, C12 OL  ,True,134
+POPC,85, H2R POPC, H2R OL  ,True,134
+POPC,86, H2S POPC, H2S OL  ,True,134
+POPC,87, C23 POPC, C13 OL  ,True,134
+POPC,88, H3R POPC, H3R OL  ,True,134
+POPC,89, H3S POPC, H3S OL  ,True,134
+POPC,90, C24 POPC, C14 OL  ,True,134
+POPC,91, H4R POPC, H4R OL  ,True,134
+POPC,92, H4S POPC, H4S OL  ,True,134
+POPC,93, C25 POPC, C15 OL  ,True,134
+POPC,94, H5R POPC, H5R OL  ,True,134
+POPC,95, H5S POPC, H5S OL  ,True,134
+POPC,96, C26 POPC, C16 OL  ,True,134
+POPC,97, H6R POPC, H6R OL  ,True,134
+POPC,98, H6S POPC, H6S OL  ,True,134
+POPC,99, C27 POPC, C17 OL  ,True,134
+POPC,100, H7R POPC, H7R OL  ,True,134
+POPC,101, H7S POPC, H7S OL  ,True,134
+POPC,102, C28 POPC, C18 OL  ,True,134
+POPC,103, H8R POPC, H8R OL  ,True,134
+POPC,104, H8S POPC, H8S OL  ,True,134
+POPC,105, C29 POPC, C19 OL  ,True,134
+POPC,106, H91 POPC, H9R OL  ,True,134
+POPC,107,C210 POPC,C110 OL  ,True,134
+POPC,108,H101 POPC,H10R OL  ,True,134
+POPC,109,C211 POPC,C111 OL  ,True,134
+POPC,110,H11R POPC,H11R OL  ,True,134
+POPC,111,H11S POPC,H11S OL  ,True,134
+POPC,112,C212 POPC,C112 OL  ,True,134
+POPC,113,H12R POPC,H12R OL  ,True,134
+POPC,114,H12S POPC,H12S OL  ,True,134
+POPC,115,C213 POPC,C113 OL  ,True,134
+POPC,116,H13R POPC,H13R OL  ,True,134
+POPC,117,H13S POPC,H13S OL  ,True,134
+POPC,118,C214 POPC,C114 OL  ,True,134
+POPC,119,H14R POPC,H14R OL  ,True,134
+POPC,120,H14S POPC,H14S OL  ,True,134
+POPC,121,C215 POPC,C115 OL  ,True,134
+POPC,122,H15R POPC,H15R OL  ,True,134
+POPC,123,H15S POPC,H15S OL  ,True,134
+POPC,124,C216 POPC,C116 OL  ,True,134
+POPC,125,H16R POPC,H16R OL  ,True,134
+POPC,126,H16S POPC,H16S OL  ,True,134
+POPC,127,C217 POPC,C117 OL  ,True,134
+POPC,128,H17R POPC,H17R OL  ,True,134
+POPC,129,H17S POPC,H17S OL  ,True,134
+POPC,130,C218 POPC,C118 OL  ,True,134
+POPC,131,H18R POPC,H18R OL  ,True,134
+POPC,132,H18S POPC,H18S OL  ,True,134
+POPC,133,H18T POPC,H18T OL  ,True,134