Sat Oct 15 15:10:07 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 15 2011 at 15:10:07 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2841 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6451496 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -5.062000 45.93300 ymin,ymax (A): 14.48800 65.47800 zmin,zma (A): -13.45300 41.72800 x,y,z range (A): 50.99500 50.99000 55.18100 scale (grids/A): 0.6451496 object centre (A): 20.43550 39.98300 14.13750 number of atom coordinates read : 2841 total number of charged atoms : 2688 net assigned charge : 4.140018 assigned positive charge : 429.1156 centred at (gu) : 90.22997 88.53646 89.15429 assigned negative charge : -424.9763 centred at (gu) : 90.04823 88.73201 89.21909 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7849 nv = 96 ne = 84 npr = 57232 no. pairs analyzed = 57232 no. exposed pairs = 3517 no. arc points = 24574 no. surface atoms = 1179 nbur = 1662 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 472 mr = 4375 m= 2 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3891 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2468 ## 224 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9558 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8935811E-08 -2.5839264E-09 midg,1,midg; midg,igrid,midg 4.7260201E-08 -1.6609558E-08 1,midg,midg; igrid,midg,midg -1.9740998E-08 3.4143891E-08 gauss-seidel spectral radius is 0.9875707 estimated iterations to convergence 73 setup time was (sec) 0.4500000 now iterating at: 15:10:08 rms-change max change #iterations 0.1622104 23.88380 at 10iterations 1.6392551E-02 2.515453 at 20iterations 1.7612588E-03 0.2206955 at 30iterations 3.2287152E-04 4.8515320E-02 at 40iterations 1.1264014E-04 1.7835617E-02 at 50iterations finished qdiffx linear iterations at : 15:10:11 total time elapsed so far: 3.940000 # loops : 50 mean,max change (kT/e) : 1.1264014E-04 1.7835617E-02 energy calculations done at 3.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.070000 DelPhi exited at 15:10:12 4.076u 0.269s 0:04.69 92.3% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 15 2011 at 15:10:12 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2841 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.935449 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -5.062000 45.93300 ymin,ymax (A): 14.48800 65.47800 zmin,zma (A): -13.45300 41.72800 x,y,z range (A): 50.99500 50.99000 55.18100 scale (grids/A): 1.935449 object centre (A): 20.43550 39.98300 14.13750 number of atom coordinates read : 2841 total number of charged atoms : 2688 net assigned charge : 4.140018 assigned positive charge : 429.1156 centred at (gu) : 90.68929 85.60874 87.46252 assigned negative charge : -424.9763 centred at (gu) : 90.14449 86.19564 87.65705 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 83579 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24574 grid for indexing accessible points = 1.400000 m= 32689 mr = 58158 m= 5626 mr = 24346 m= 336 mr = 3530 m= 3 mr = 108 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 151 time to turn everything in is 0.4600000 number of dielectric boundary points 36091 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 176 iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 21189 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.6451496 object centre at (A) : 20.43550 39.98300 14.13750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.6744490E-02 -8.8316230E-03 midg,1,midg; midg,igrid,midg 0.1119336 -1.9331882E-02 1,midg,midg; igrid,midg,midg -4.2231869E-02 6.7192435E-02 gauss-seidel spectral radius is 0.9987016 estimated iterations to convergence 220 setup time was (sec) 0.7400000 now iterating at: 15:10:13 rms-change max change #iterations 4.604921 228.3706 at 10iterations 2.218615 74.36644 at 20iterations 1.061558 33.66645 at 30iterations 0.5088264 15.58966 at 40iterations 0.2440288 7.808280 at 50iterations 0.1170354 3.540482 at 60iterations 5.6081142E-02 1.643899 at 70iterations 2.6903886E-02 0.8070540 at 80iterations 1.2885588E-02 0.3868160 at 90iterations 6.2347869E-03 0.1931858 at 100iterations 3.0230440E-03 8.8308334E-02 at 110iterations 1.5023433E-03 4.5889854E-02 at 120iterations finished qdiffx linear iterations at : 15:10:21 total time elapsed so far: 9.440000 # loops : 120 mean,max change (kT/e) : 1.5023433E-03 4.5889854E-02 energy calculations done at 9.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.580000 DelPhi exited at 15:10:22 9.578u 0.304s 0:10.28 96.0% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 15 2011 at 15:10:22 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2841 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.903173 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -5.062000 45.93300 ymin,ymax (A): 14.48800 65.47800 zmin,zma (A): -13.45300 41.72800 x,y,z range (A): 50.99500 50.99000 55.18100 scale (grids/A): 2.903173 object centre (A): 20.43550 39.98300 14.13750 number of atom coordinates read : 2841 total number of charged atoms : 2688 net assigned charge : 4.140018 assigned positive charge : 429.1156 centred at (gu) : 91.03370 83.41296 86.19366 assigned negative charge : -424.9763 centred at (gu) : 90.21676 84.29356 86.48554 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 192794 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24574 grid for indexing accessible points = 1.400000 m= 102790 mr = 140459 m= 40269 mr = 84624 m= 10336 mr = 32557 m= 1456 mr = 7700 m= 83 mr = 878 m= 0 mr = 30 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 488 time to turn everything in is 1.180000 number of dielectric boundary points 81480 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 21500 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.935449 object centre at (A) : 20.43550 39.98300 14.13750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.9731492 5.6119617E-02 midg,1,midg; midg,igrid,midg 1.153508 -9.8215707E-02 1,midg,midg; igrid,midg,midg -0.6200286 0.7689729 gauss-seidel spectral radius is 0.9992822 estimated iterations to convergence 295 setup time was (sec) 1.500000 now iterating at: 15:10:24 rms-change max change #iterations 10.72491 328.8669 at 10iterations 6.337472 135.6077 at 20iterations 3.723745 70.54021 at 30iterations 2.182345 37.63525 at 40iterations 1.274950 24.18340 at 50iterations 0.7450658 13.08714 at 60iterations 0.4344018 7.905025 at 70iterations 0.2531013 4.300674 at 80iterations 0.1472088 2.570567 at 90iterations 8.5620388E-02 1.429108 at 100iterations 4.9772348E-02 0.9048171 at 110iterations 2.8862905E-02 0.5315247 at 120iterations 1.6812388E-02 0.3027344 at 130iterations 9.7674187E-03 0.1681118 at 140iterations 5.6875939E-03 9.4018936E-02 at 150iterations 3.3243268E-03 5.8977127E-02 at 160iterations 1.9574468E-03 3.3817291E-02 at 170iterations 1.1746617E-03 2.2069931E-02 at 180iterations finished qdiffx linear iterations at : 15:10:38 total time elapsed so far: 15.41000 # loops : 180 mean,max change (kT/e) : 1.1746617E-03 2.2069931E-02 energy calculations done at 15.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.55000 DelPhi exited at 15:10:38 15.549u 0.299s 0:16.26 97.3% 0+0k 0+0io 0pf+0w