Sun Oct 9 09:36:03 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+sph2.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 = amb2.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 Sun Oct 9 2011 at 09:36:03 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2605 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5868486 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): -80.28700 -31.56800 ymin,ymax (A): -33.03900 27.62400 zmin,zma (A): -51.83400 7.309000 x,y,z range (A): 48.71900 60.66300 59.14300 scale (grids/A): 0.5868486 object centre (A): -55.92750 -2.707500 -22.26250 number of atom coordinates read : 2605 total number of charged atoms : 2462 net assigned charge : 1.8335879E-05 assigned positive charge : 384.7108 centred at (gu) : 89.26679 88.75906 88.05669 assigned negative charge : -384.7115 centred at (gu) : 89.25221 88.97695 88.11496 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6093 nv = 96 ne = 84 npr = 50976 no. pairs analyzed = 50976 no. exposed pairs = 3620 no. arc points = 26308 no. surface atoms = 1204 nbur = 1401 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 300 mr = 2945 m= 2 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3430 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2665 ## 323 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7640 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0344364E-09 -9.4302277E-10 midg,1,midg; midg,igrid,midg 6.6358763E-09 -4.0320249E-09 1,midg,midg; igrid,midg,midg -5.2224097E-10 2.1244285E-10 gauss-seidel spectral radius is 0.9849919 estimated iterations to convergence 67 setup time was (sec) 0.5200000 now iterating at: 09:36:04 rms-change max change #iterations 9.9129051E-02 16.53416 at 10iterations 7.7831582E-03 1.413606 at 20iterations 6.2383479E-04 0.1072941 at 30iterations 5.0839481E-05 8.4381104E-03 at 40iterations 4.0192940E-06 7.3623657E-04 at 50iterations finished qdiffx linear iterations at : 09:36:07 total time elapsed so far: 3.110000 # loops : 50 mean,max change (kT/e) : 4.0192940E-06 7.3623657E-04 energy calculations done at 3.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.280000 DelPhi exited at 09:36:07 3.280u 0.200s 0:03.76 92.5% 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 Sun Oct 9 2011 at 09:36:07 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2605 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.760546 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): -80.28700 -31.56800 ymin,ymax (A): -33.03900 27.62400 zmin,zma (A): -51.83400 7.309000 x,y,z range (A): 48.71900 60.66300 59.14300 scale (grids/A): 1.760546 object centre (A): -55.92750 -2.707500 -22.26250 number of atom coordinates read : 2605 total number of charged atoms : 2462 net assigned charge : 1.8335879E-05 assigned positive charge : 384.7108 centred at (gu) : 87.79983 86.27644 84.16950 assigned negative charge : -384.7115 centred at (gu) : 87.75652 86.93085 84.34466 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 65989 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26308 grid for indexing accessible points = 1.400000 m= 22103 mr = 42815 m= 2903 mr = 15120 m= 122 mr = 1457 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 267 time to turn everything in is 0.4900000 number of dielectric boundary points 31708 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 224 iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 19236 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) : 0.5868486 object centre at (A) : -55.92750 -2.707500 -22.26250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.8219902E-03 -9.8290516E-04 midg,1,midg; midg,igrid,midg 4.1471510E-03 -2.2303987E-02 1,midg,midg; igrid,midg,midg 1.0643973E-02 7.8098150E-03 gauss-seidel spectral radius is 0.9984199 estimated iterations to convergence 200 setup time was (sec) 0.7800000 now iterating at: 09:36:08 rms-change max change #iterations 3.604275 178.3121 at 10iterations 1.576781 64.04937 at 20iterations 0.6964999 28.98309 at 30iterations 0.3076595 10.30976 at 40iterations 0.1350263 4.643955 at 50iterations 5.9635092E-02 2.115395 at 60iterations 2.6166484E-02 0.9606953 at 70iterations 1.1605827E-02 0.4286079 at 80iterations 5.1176939E-03 0.1777153 at 90iterations 2.2611646E-03 7.6637268E-02 at 100iterations 9.9838746E-04 3.4103394E-02 at 110iterations 4.3918157E-04 1.4440536E-02 at 120iterations finished qdiffx linear iterations at : 09:36:15 total time elapsed so far: 7.330000 # loops : 120 mean,max change (kT/e) : 4.3918157E-04 1.4440536E-02 energy calculations done at 7.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.500000 DelPhi exited at 09:36:15 7.504u 0.241s 0:08.07 95.9% 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 Sun Oct 9 2011 at 09:36:15 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2605 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.640819 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): -80.28700 -31.56800 ymin,ymax (A): -33.03900 27.62400 zmin,zma (A): -51.83400 7.309000 x,y,z range (A): 48.71900 60.66300 59.14300 scale (grids/A): 2.640819 object centre (A): -55.92750 -2.707500 -22.26250 number of atom coordinates read : 2605 total number of charged atoms : 2462 net assigned charge : 1.8335879E-05 assigned positive charge : 384.7108 centred at (gu) : 86.69968 84.41442 81.25418 assigned negative charge : -384.7115 centred at (gu) : 86.63467 85.39631 81.51700 start vw surface at 0.1700000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 152631 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26308 grid for indexing accessible points = 1.400000 m= 72004 mr = 104610 m= 23968 mr = 56381 m= 4788 mr = 18053 m= 467 mr = 3090 m= 9 mr = 219 m= 0 mr = 0 time to grow re-entrant surface = 0.6800001 no. cavity mid-points inaccessible to solvent = 864 time to turn everything in is 1.220000 number of dielectric boundary points 71514 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 19687 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) : 1.760546 object centre at (A) : -55.92750 -2.707500 -22.26250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.8512445E-02 -5.3045422E-02 midg,1,midg; midg,igrid,midg -6.4058639E-02 -9.8639399E-02 1,midg,midg; igrid,midg,midg 0.1436840 0.1248188 gauss-seidel spectral radius is 0.9992065 estimated iterations to convergence 280 setup time was (sec) 1.540000 now iterating at: 09:36:17 rms-change max change #iterations 9.042224 282.7511 at 10iterations 5.247139 126.0986 at 20iterations 3.009490 73.80483 at 30iterations 1.716262 37.58312 at 40iterations 0.9770603 21.33223 at 50iterations 0.5536734 10.92373 at 60iterations 0.3134353 6.488192 at 70iterations 0.1772590 3.955368 at 80iterations 0.1000133 2.020741 at 90iterations 5.6365348E-02 1.248928 at 100iterations 3.1805240E-02 0.6818161 at 110iterations 1.7907206E-02 0.3407211 at 120iterations 1.0064364E-02 0.2034149 at 130iterations 5.6725875E-03 0.1132030 at 140iterations 3.1964206E-03 6.5863848E-02 at 150iterations 1.7979097E-03 3.6582947E-02 at 160iterations 1.0134473E-03 1.9927979E-02 at 170iterations 5.7092425E-04 1.0979652E-02 at 180iterations finished qdiffx linear iterations at : 09:36:27 total time elapsed so far: 11.95000 # loops : 180 mean,max change (kT/e) : 5.7092425E-04 1.0979652E-02 energy calculations done at 11.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.13000 DelPhi exited at 09:36:28 12.129u 0.219s 0:12.69 97.1% 0+0k 0+0io 0pf+0w