Tue Nov 22 14:10:11 PST 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 Tue Nov 22 2011 at 14:10:15 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5921687 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): -35.15600 11.15000 ymin,ymax (A): 1.020000 41.79800 zmin,zma (A): -1.288000 58.83000 x,y,z range (A): 46.30600 40.77800 60.11800 scale (grids/A): 0.5921687 object centre (A): -12.00300 21.40900 28.77100 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 289.4000 centred at (gu) : 90.16116 89.37057 89.43395 assigned negative charge : -286.4003 centred at (gu) : 90.06350 89.51981 89.43513 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 4677 nv = 96 ne = 84 npr = 40042 no. pairs analyzed = 40042 no. exposed pairs = 2460 no. arc points = 17136 no. surface atoms = 841 nbur = 1129 mkacc time = 9.0000004E-02 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= 223 mr = 2565 m= 2 mr = 12 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 0.2500000 number of dielectric boundary points 2325 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1778 ## 186 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 5777 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1285507E-09 8.3406404E-10 midg,1,midg; midg,igrid,midg 4.6972382E-09 -1.9181776E-09 1,midg,midg; igrid,midg,midg -1.0677356E-09 3.1170770E-09 gauss-seidel spectral radius is 0.9851928 estimated iterations to convergence 67 setup time was (sec) 0.5200000 now iterating at: 14:10:19 rms-change max change #iterations 8.6635716E-02 17.05570 at 10iterations 7.2024767E-03 1.278862 at 20iterations 5.8964628E-04 0.1035442 at 30iterations 4.7701895E-05 9.6240044E-03 at 40iterations 3.8967960E-06 8.2015991E-04 at 50iterations finished qdiffx linear iterations at : 14:10:27 total time elapsed so far: 3.450000 # loops : 50 mean,max change (kT/e) : 3.8967960E-06 8.2015991E-04 energy calculations done at 3.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.640000 DelPhi exited at 14:10:29 3.647u 0.194s 0:15.28 25.0% 0+0k 0+0io 3pf+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 Tue Nov 22 2011 at 14:10:32 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.776506 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): -35.15600 11.15000 ymin,ymax (A): 1.020000 41.79800 zmin,zma (A): -1.288000 58.83000 x,y,z range (A): 46.30600 40.77800 60.11800 scale (grids/A): 1.776506 object centre (A): -12.00300 21.40900 28.77100 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 289.4000 centred at (gu) : 90.48315 88.11163 88.30177 assigned negative charge : -286.4003 centred at (gu) : 90.19061 88.55988 88.30550 start vw surface at 0.1300000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 50612 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17136 grid for indexing accessible points = 1.400000 m= 17666 mr = 34555 m= 2329 mr = 13176 m= 99 mr = 1387 m= 1 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 334 time to turn everything in is 0.4100000 number of dielectric boundary points 21562 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 172 iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 14316 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) : 0.5921687 object centre at (A) : -12.00300 21.40900 28.77100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1388672E-02 2.3245074E-02 midg,1,midg; midg,igrid,midg 2.8579775E-03 -6.6589406E-03 1,midg,midg; igrid,midg,midg -1.3835620E-03 3.4535653E-04 gauss-seidel spectral radius is 0.9983572 estimated iterations to convergence 196 setup time was (sec) 0.7300000 now iterating at: 14:10:37 rms-change max change #iterations 3.099372 149.2390 at 10iterations 1.344332 61.42313 at 20iterations 0.5850043 26.66437 at 30iterations 0.2540870 9.851851 at 40iterations 0.1103581 4.665482 at 50iterations 4.8005011E-02 1.919277 at 60iterations 2.0877833E-02 0.8240681 at 70iterations 9.0692108E-03 0.3398085 at 80iterations 3.9453702E-03 0.1547031 at 90iterations 1.7186553E-03 6.9058418E-02 at 100iterations 7.4648455E-04 2.8873444E-02 at 110iterations 3.2599282E-04 1.2065887E-02 at 120iterations finished qdiffx linear iterations at : 14:10:59 total time elapsed so far: 7.990000 # loops : 120 mean,max change (kT/e) : 3.2599282E-04 1.2065887E-02 energy calculations done at 7.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.180000 DelPhi exited at 14:11:01 8.181u 0.259s 0:28.96 29.1% 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 Tue Nov 22 2011 at 14:11:01 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 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: 2.664759 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): -35.15600 11.15000 ymin,ymax (A): 1.020000 41.79800 zmin,zma (A): -1.288000 58.83000 x,y,z range (A): 46.30600 40.77800 60.11800 scale (grids/A): 2.664759 object centre (A): -12.00300 21.40900 28.77100 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 289.4000 centred at (gu) : 90.72470 87.16756 87.45264 assigned negative charge : -286.4003 centred at (gu) : 90.28598 87.83985 87.45840 start vw surface at 0.1200000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 117018 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17136 grid for indexing accessible points = 1.400000 m= 57989 mr = 83691 m= 20000 mr = 47612 m= 3923 mr = 16257 m= 443 mr = 2881 m= 19 mr = 262 m= 0 mr = 11 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 1151 time to turn everything in is 0.9800000 number of dielectric boundary points 48678 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 14702 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) : 1.776506 object centre at (A) : -12.00300 21.40900 28.77100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.1914172E-03 0.2191794 midg,1,midg; midg,igrid,midg -4.0431647E-03 -0.1006945 1,midg,midg; igrid,midg,midg -4.2860013E-02 -3.3218917E-02 gauss-seidel spectral radius is 0.9991588 estimated iterations to convergence 272 setup time was (sec) 1.320000 now iterating at: 14:11:04 rms-change max change #iterations 7.549626 311.2328 at 10iterations 4.215236 128.6730 at 20iterations 2.350298 61.58250 at 30iterations 1.301635 31.32434 at 40iterations 0.7185026 15.61802 at 50iterations 0.3985085 9.554575 at 60iterations 0.2196497 4.826305 at 70iterations 0.1216687 2.727682 at 80iterations 6.7079470E-02 1.628140 at 90iterations 3.7140328E-02 0.8284578 at 100iterations 2.0514393E-02 0.4823437 at 110iterations 1.1309082E-02 0.2587557 at 120iterations 6.2460368E-03 0.1509199 at 130iterations 3.4575108E-03 7.9330444E-02 at 140iterations 1.9089346E-03 4.1877747E-02 at 150iterations 1.0544661E-03 2.1862030E-02 at 160iterations 5.8213936E-04 1.2416840E-02 at 170iterations 3.2190952E-04 7.5607300E-03 at 180iterations finished qdiffx linear iterations at : 14:11:34 total time elapsed so far: 14.73000 # loops : 180 mean,max change (kT/e) : 3.2190952E-04 7.5607300E-03 energy calculations done at 14.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.92000 DelPhi exited at 14:11:36 14.921u 0.227s 0:34.59 43.7% 0+0k 0+0io 0pf+0w