Tue Oct 11 06:20:29 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 Tue Oct 11 2011 at 06:20:29 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2076 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6939706 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): -9.811000 36.70900 ymin,ymax (A): -3.245000 34.80500 zmin,zma (A): 0.2110000 51.51000 x,y,z range (A): 46.52000 38.05000 51.29900 scale (grids/A): 0.6939706 object centre (A): 13.44900 15.78000 25.86050 number of atom coordinates read : 2076 total number of charged atoms : 1945 net assigned charge : 5.039006 assigned positive charge : 317.6830 centred at (gu) : 89.52056 89.30169 90.15482 assigned negative charge : -312.6441 centred at (gu) : 89.40382 89.37435 90.17931 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6694 nv = 96 ne = 84 npr = 42224 no. pairs analyzed = 42224 no. exposed pairs = 2431 no. arc points = 16728 no. surface atoms = 829 nbur = 1247 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 434 mr = 3865 m= 2 mr = 95 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 3170 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1629 ## 151 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7609 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.8535063E-08 2.2487313E-08 midg,1,midg; midg,igrid,midg 6.5551738E-08 3.7866830E-09 1,midg,midg; igrid,midg,midg -1.3739601E-08 6.6287896E-08 gauss-seidel spectral radius is 0.9891773 estimated iterations to convergence 78 setup time was (sec) 0.3700000 now iterating at: 06:20:29 rms-change max change #iterations 0.1940577 26.05538 at 10iterations 2.2986988E-02 3.074726 at 20iterations 2.9871385E-03 0.4085908 at 30iterations 4.7565351E-04 5.8258057E-02 at 40iterations 1.1091628E-04 1.3364792E-02 at 50iterations finished qdiffx linear iterations at : 06:20:32 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 1.1091628E-04 1.3364792E-02 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 06:20:33 3.461u 0.175s 0:04.08 88.9% 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 Tue Oct 11 2011 at 06:20:33 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2076 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.081912 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): -9.811000 36.70900 ymin,ymax (A): -3.245000 34.80500 zmin,zma (A): 0.2110000 51.51000 x,y,z range (A): 46.52000 38.05000 51.29900 scale (grids/A): 2.081912 object centre (A): 13.44900 15.78000 25.86050 number of atom coordinates read : 2076 total number of charged atoms : 1945 net assigned charge : 5.039006 assigned positive charge : 317.6830 centred at (gu) : 88.56170 87.90483 90.46433 assigned negative charge : -312.6441 centred at (gu) : 88.21142 88.12311 90.53789 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 71778 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16728 grid for indexing accessible points = 1.400000 m= 28198 mr = 51357 m= 5187 mr = 21342 m= 425 mr = 3399 m= 7 mr = 212 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 29285 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 84 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 15411 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) : 0.6939706 object centre at (A) : 13.44900 15.78000 25.86050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.7712663E-02 4.0859658E-02 midg,1,midg; midg,igrid,midg 3.1034544E-02 -5.3187925E-03 1,midg,midg; igrid,midg,midg 1.3597026E-02 2.6522599E-02 gauss-seidel spectral radius is 0.9987866 estimated iterations to convergence 227 setup time was (sec) 0.6000000 now iterating at: 06:20:34 rms-change max change #iterations 4.515334 217.9808 at 10iterations 2.204739 69.77476 at 20iterations 1.079514 36.23343 at 30iterations 0.5319383 16.13731 at 40iterations 0.2603500 7.981216 at 50iterations 0.1275958 3.725216 at 60iterations 6.2673397E-02 1.873291 at 70iterations 3.0860439E-02 0.9327831 at 80iterations 1.5214448E-02 0.5482768 at 90iterations 7.5402367E-03 0.2329102 at 100iterations 3.7595606E-03 0.1371765 at 110iterations 1.9129943E-03 5.8925629E-02 at 120iterations finished qdiffx linear iterations at : 06:20:41 total time elapsed so far: 7.960000 # loops : 120 mean,max change (kT/e) : 1.9129943E-03 5.8925629E-02 energy calculations done at 7.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.090000 DelPhi exited at 06:20:42 8.094u 0.203s 0:08.86 93.5% 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 Tue Oct 11 2011 at 06:20:42 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2076 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.122868 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): -9.811000 36.70900 ymin,ymax (A): -3.245000 34.80500 zmin,zma (A): 0.2110000 51.51000 x,y,z range (A): 46.52000 38.05000 51.29900 scale (grids/A): 3.122868 object centre (A): 13.44900 15.78000 25.86050 number of atom coordinates read : 2076 total number of charged atoms : 1945 net assigned charge : 5.039006 assigned positive charge : 317.6830 centred at (gu) : 87.84256 86.85730 90.69643 assigned negative charge : -312.6441 centred at (gu) : 87.31721 87.18455 90.80690 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 165754 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16728 grid for indexing accessible points = 1.400000 m= 89341 mr = 123857 m= 34918 mr = 74409 m= 9556 mr = 28575 m= 1750 mr = 7346 m= 217 mr = 1242 m= 7 mr = 139 m= 0 mr = 0 time to grow re-entrant surface = 0.5600001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.110000 number of dielectric boundary points 65975 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 15556 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) : 2.081912 object centre at (A) : 13.44900 15.78000 25.86050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3222370 0.3685013 midg,1,midg; midg,igrid,midg 0.2740076 -4.1619871E-02 1,midg,midg; igrid,midg,midg 0.2542651 0.2499518 gauss-seidel spectral radius is 0.9992802 estimated iterations to convergence 294 setup time was (sec) 1.370000 now iterating at: 06:20:44 rms-change max change #iterations 10.12557 334.6185 at 10iterations 5.954206 207.3777 at 20iterations 3.494680 68.04426 at 30iterations 2.048562 42.65390 at 40iterations 1.198673 22.93376 at 50iterations 0.6998003 13.07662 at 60iterations 0.4081315 8.093823 at 70iterations 0.2383406 4.303064 at 80iterations 0.1386529 2.483360 at 90iterations 8.0966204E-02 1.488050 at 100iterations 4.7208909E-02 0.9134712 at 110iterations 2.7734319E-02 0.4774857 at 120iterations 1.6357603E-02 0.2972412 at 130iterations 9.8079173E-03 0.1802216 at 140iterations 5.9972145E-03 0.1191330 at 150iterations 3.7974841E-03 7.9643250E-02 at 160iterations 2.5312791E-03 4.8843384E-02 at 170iterations 1.7864077E-03 3.6922455E-02 at 180iterations finished qdiffx linear iterations at : 06:20:55 total time elapsed so far: 12.95000 # loops : 180 mean,max change (kT/e) : 1.7864077E-03 3.6922455E-02 energy calculations done at 12.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.08000 DelPhi exited at 06:20:56 13.084u 0.202s 0:13.61 97.5% 0+0k 0+0io 0pf+0w