Mon Oct 10 00:54:58 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 Mon Oct 10 2011 at 00:54:58 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2047 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: 0.7344295 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): -9.436000 38.61000 ymin,ymax (A): -52.17900 -3.706000 zmin,zma (A): -22.47300 21.45200 x,y,z range (A): 48.04600 48.47300 43.92500 scale (grids/A): 0.7344295 object centre (A): 14.58700 -27.94250 -0.5105000 number of atom coordinates read : 2047 total number of charged atoms : 1906 net assigned charge : 2.000008 assigned positive charge : 303.2678 centred at (gu) : 89.16496 88.66958 90.22361 assigned negative charge : -301.2680 centred at (gu) : 89.07130 88.71583 90.30806 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7772 nv = 96 ne = 84 npr = 40623 no. pairs analyzed = 40623 no. exposed pairs = 2885 no. arc points = 19431 no. surface atoms = 974 nbur = 1073 mkacc time = 7.0000000E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 619 mr = 4162 m= 6 mr = 128 m= 0 mr = 0 time to grow re-entrant surface = 8.0000006E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 4107 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1510 ## 99 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8067 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.8586725E-08 -4.2774534E-08 midg,1,midg; midg,igrid,midg 9.1051021E-08 -5.7831935E-09 1,midg,midg; igrid,midg,midg -5.7829787E-08 9.4421964E-08 gauss-seidel spectral radius is 0.9903398 estimated iterations to convergence 83 setup time was (sec) 0.3700000 now iterating at: 00:54:59 rms-change max change #iterations 0.2368830 34.52048 at 10iterations 3.0891690E-02 4.216717 at 20iterations 4.1049812E-03 0.4900107 at 30iterations 5.4746220E-04 7.4359894E-02 at 40iterations 7.1387549E-05 9.3078613E-03 at 50iterations finished qdiffx linear iterations at : 00:55:02 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 7.1387549E-05 9.3078613E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 00:55:02 3.392u 0.157s 0:03.91 90.5% 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 Mon Oct 10 2011 at 00:55:02 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2047 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: 2.203289 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): -9.436000 38.61000 ymin,ymax (A): -52.17900 -3.706000 zmin,zma (A): -22.47300 21.45200 x,y,z range (A): 48.04600 48.47300 43.92500 scale (grids/A): 2.203289 object centre (A): 14.58700 -27.94250 -0.5105000 number of atom coordinates read : 2047 total number of charged atoms : 1906 net assigned charge : 2.000008 assigned positive charge : 303.2678 centred at (gu) : 87.49485 86.00848 90.67052 assigned negative charge : -301.2680 centred at (gu) : 87.21400 86.14743 90.92412 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 81751 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19431 grid for indexing accessible points = 1.400000 m= 32358 mr = 55612 m= 7488 mr = 23688 m= 866 mr = 5090 m= 39 mr = 474 m= 0 mr = 10 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 37628 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 50 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 15193 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) : 0.7344295 object centre at (A) : 14.58700 -27.94250 -0.5105000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.4884057E-02 2.5813324E-02 midg,1,midg; midg,igrid,midg -5.4893936E-03 -5.0532028E-02 1,midg,midg; igrid,midg,midg 1.8278478E-02 1.2390763E-02 gauss-seidel spectral radius is 0.9989196 estimated iterations to convergence 241 setup time was (sec) 0.6500000 now iterating at: 00:55:03 rms-change max change #iterations 4.907853 190.4253 at 10iterations 2.495144 91.31338 at 20iterations 1.264441 39.31956 at 30iterations 0.6428180 19.29121 at 40iterations 0.3278303 9.678936 at 50iterations 0.1666810 4.739624 at 60iterations 8.4803484E-02 2.594810 at 70iterations 4.2987134E-02 1.205391 at 80iterations 2.1947622E-02 0.6800842 at 90iterations 1.1171503E-02 0.3093681 at 100iterations 5.6796069E-03 0.1544380 at 110iterations 2.8919308E-03 8.0883026E-02 at 120iterations finished qdiffx linear iterations at : 00:55:10 total time elapsed so far: 7.840000 # loops : 120 mean,max change (kT/e) : 2.8919308E-03 8.0883026E-02 energy calculations done at 7.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.970000 DelPhi exited at 00:55:11 7.969u 0.200s 0:08.58 95.1% 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 Mon Oct 10 2011 at 00:55:11 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2047 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: 3.304933 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): -9.436000 38.61000 ymin,ymax (A): -52.17900 -3.706000 zmin,zma (A): -22.47300 21.45200 x,y,z range (A): 48.04600 48.47300 43.92500 scale (grids/A): 3.304933 object centre (A): 14.58700 -27.94250 -0.5105000 number of atom coordinates read : 2047 total number of charged atoms : 1906 net assigned charge : 2.000008 assigned positive charge : 303.2678 centred at (gu) : 86.24233 84.01274 91.00574 assigned negative charge : -301.2680 centred at (gu) : 85.82104 84.22114 91.38631 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 188162 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19431 grid for indexing accessible points = 1.400000 m= 98091 mr = 134330 m= 43119 mr = 79624 m= 14432 mr = 34883 m= 3299 mr = 11247 m= 502 mr = 2474 m= 40 mr = 362 m= 0 mr = 11 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.290000 number of dielectric boundary points 84714 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 15248 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) : 2.203289 object centre at (A) : 14.58700 -27.94250 -0.5105000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8884838 0.2323459 midg,1,midg; midg,igrid,midg -0.1541209 -0.6285896 1,midg,midg; igrid,midg,midg 0.2298715 0.2247213 gauss-seidel spectral radius is 0.9993343 estimated iterations to convergence 306 setup time was (sec) 1.520000 now iterating at: 00:55:12 rms-change max change #iterations 10.76818 279.7332 at 10iterations 6.480763 151.4807 at 20iterations 3.896105 81.42035 at 30iterations 2.327137 44.55210 at 40iterations 1.389382 23.69325 at 50iterations 0.8286694 14.04721 at 60iterations 0.4922121 8.647539 at 70iterations 0.2927081 4.781220 at 80iterations 0.1738762 3.000202 at 90iterations 0.1029559 1.668869 at 100iterations 6.1001230E-02 1.121719 at 110iterations 3.6166564E-02 0.5967197 at 120iterations 2.1464756E-02 0.3544455 at 130iterations 1.2672878E-02 0.2166119 at 140iterations 7.5041605E-03 0.1260376 at 150iterations 4.4467272E-03 7.9343319E-02 at 160iterations 2.6269408E-03 4.4336319E-02 at 170iterations 1.5575634E-03 2.4791718E-02 at 180iterations finished qdiffx linear iterations at : 00:55:24 total time elapsed so far: 13.15000 # loops : 180 mean,max change (kT/e) : 1.5575634E-03 2.4791718E-02 energy calculations done at 13.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.28000 DelPhi exited at 00:55:25 13.279u 0.212s 0:13.81 97.6% 0+0k 0+0io 0pf+0w