Sat Oct 8 18:36:09 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 Sat Oct 8 2011 at 18:36:09 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2583 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: PHE 260 has a net charge of 0.5000 !!! WARNING: ZN5 556 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6376842 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): -31.66800 17.37000 ymin,ymax (A): -22.96200 23.09900 zmin,zma (A): -11.96800 43.85900 x,y,z range (A): 49.03800 46.06100 55.82700 scale (grids/A): 0.6376842 object centre (A): -7.149000 6.8499565E-02 15.94550 number of atom coordinates read : 2583 total number of charged atoms : 2449 net assigned charge : 4.406008 assigned positive charge : 391.8441 centred at (gu) : 88.43881 88.94307 89.95142 assigned negative charge : -387.4385 centred at (gu) : 88.36213 89.01102 89.82124 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6842 nv = 96 ne = 84 npr = 54277 no. pairs analyzed = 54277 no. exposed pairs = 2909 no. arc points = 20930 no. surface atoms = 991 nbur = 1592 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 333 mr = 3949 m= 2 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 115 time to turn everything in is 0.3000000 number of dielectric boundary points 3192 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2113 ## 197 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8397 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.4122753E-09 1.9829114E-08 midg,1,midg; midg,igrid,midg 1.6827986E-08 -1.0481704E-09 1,midg,midg; igrid,midg,midg -3.4922170E-09 1.0300798E-08 gauss-seidel spectral radius is 0.9872516 estimated iterations to convergence 72 setup time was (sec) 0.6000000 now iterating at: 18:36:10 rms-change max change #iterations 0.1474302 21.14289 at 10iterations 1.4418631E-02 2.301817 at 20iterations 1.4145891E-03 0.2387962 at 30iterations 1.4142104E-04 1.9121170E-02 at 40iterations 1.3822819E-05 1.9569397E-03 at 50iterations finished qdiffx linear iterations at : 18:36:13 total time elapsed so far: 4.260000 # loops : 50 mean,max change (kT/e) : 1.3822819E-05 1.9569397E-03 energy calculations done at 4.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.440000 DelPhi exited at 18:36:14 4.449u 0.398s 0:05.12 94.3% 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 8 2011 at 18:36:14 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2583 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: PHE 260 has a net charge of 0.5000 !!! WARNING: ZN5 556 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.913053 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): -31.66800 17.37000 ymin,ymax (A): -22.96200 23.09900 zmin,zma (A): -11.96800 43.85900 x,y,z range (A): 49.03800 46.06100 55.82700 scale (grids/A): 1.913053 object centre (A): -7.149000 6.8499565E-02 15.94550 number of atom coordinates read : 2583 total number of charged atoms : 2449 net assigned charge : 4.406008 assigned positive charge : 391.8441 centred at (gu) : 85.31581 86.82877 89.85406 assigned negative charge : -387.4385 centred at (gu) : 85.08595 87.03313 89.46358 start vw surface at 0.1100000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 74497 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20930 grid for indexing accessible points = 1.400000 m= 26747 mr = 52860 m= 4116 mr = 20311 m= 229 mr = 2658 m= 4 mr = 110 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 2193 time to turn everything in is 0.5900000 number of dielectric boundary points 29654 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 133 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 19282 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) : 0.6376842 object centre at (A) : -7.149000 6.8499565E-02 15.94550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9249434E-02 2.3191566E-02 midg,1,midg; midg,igrid,midg 1.9979838E-02 -1.1388585E-03 1,midg,midg; igrid,midg,midg -1.6983730E-03 3.4263220E-02 gauss-seidel spectral radius is 0.9986371 estimated iterations to convergence 215 setup time was (sec) 0.9300000 now iterating at: 18:36:15 rms-change max change #iterations 4.219828 186.1281 at 10iterations 1.977785 64.94247 at 20iterations 0.9297206 30.31862 at 30iterations 0.4365677 15.38905 at 40iterations 0.2044498 6.191040 at 50iterations 9.5933422E-02 3.081900 at 60iterations 4.4978127E-02 1.431496 at 70iterations 2.1060299E-02 0.6653748 at 80iterations 9.8728994E-03 0.3199015 at 90iterations 4.6410821E-03 0.1514702 at 100iterations 2.1740503E-03 6.6089630E-02 at 110iterations 1.0202231E-03 3.7574768E-02 at 120iterations finished qdiffx linear iterations at : 18:36:25 total time elapsed so far: 10.23000 # loops : 120 mean,max change (kT/e) : 1.0202231E-03 3.7574768E-02 energy calculations done at 10.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.41000 DelPhi exited at 18:36:25 10.413u 0.457s 0:11.13 97.5% 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 Sat Oct 8 2011 at 18:36:25 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2583 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: PHE 260 has a net charge of 0.5000 !!! WARNING: ZN5 556 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.869579 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): -31.66800 17.37000 ymin,ymax (A): -22.96200 23.09900 zmin,zma (A): -11.96800 43.85900 x,y,z range (A): 49.03800 46.06100 55.82700 scale (grids/A): 2.869579 object centre (A): -7.149000 6.8499565E-02 15.94550 number of atom coordinates read : 2583 total number of charged atoms : 2449 net assigned charge : 4.406008 assigned positive charge : 391.8441 centred at (gu) : 82.97369 85.24294 89.78101 assigned negative charge : -387.4385 centred at (gu) : 82.62885 85.54957 89.19533 start vw surface at 0.1000000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 172058 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20930 grid for indexing accessible points = 1.400000 m= 87770 mr = 127223 m= 31071 mr = 73345 m= 7479 mr = 25545 m= 1123 mr = 5857 m= 77 mr = 797 m= 1 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.9300000 no. cavity mid-points inaccessible to solvent = 7199 time to turn everything in is 1.550000 number of dielectric boundary points 66773 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.690000 number of grid points assigned charge 19592 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) : 1.913053 object centre at (A) : -7.149000 6.8499565E-02 15.94550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.9016356E-02 0.2066666 midg,1,midg; midg,igrid,midg 0.2121697 -1.0003041E-02 1,midg,midg; igrid,midg,midg 1.3860863E-02 0.4187501 gauss-seidel spectral radius is 0.9992525 estimated iterations to convergence 289 setup time was (sec) 1.880000 now iterating at: 18:36:27 rms-change max change #iterations 9.825404 403.7207 at 10iterations 5.662191 132.4714 at 20iterations 3.244990 61.68439 at 30iterations 1.859930 36.89587 at 40iterations 1.064376 19.74081 at 50iterations 0.6101627 10.86777 at 60iterations 0.3488513 6.580389 at 70iterations 0.1999375 3.680264 at 80iterations 0.1142625 2.083885 at 90iterations 6.5441065E-02 1.214563 at 100iterations 3.7487444E-02 0.6951447 at 110iterations 2.1436336E-02 0.3934784 at 120iterations 1.2273487E-02 0.2306437 at 130iterations 7.0252456E-03 0.1262741 at 140iterations 4.0229633E-03 7.7401638E-02 at 150iterations 2.2994129E-03 4.6420217E-02 at 160iterations 1.3186291E-03 2.3981094E-02 at 170iterations 7.5258611E-04 1.3927460E-02 at 180iterations finished qdiffx linear iterations at : 18:36:43 total time elapsed so far: 17.38000 # loops : 180 mean,max change (kT/e) : 7.5258611E-04 1.3927460E-02 energy calculations done at 17.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.55000 DelPhi exited at 18:36:43 17.555u 0.479s 0:18.29 98.5% 0+0k 0+0io 0pf+0w