Sat Oct 8 19:46:16 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 19:46:16 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: 295 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: ZN5 547 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6209230 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): -31.52500 17.68500 ymin,ymax (A): -23.34500 23.69200 zmin,zma (A): -12.63800 44.69600 x,y,z range (A): 49.21000 47.03700 57.33400 scale (grids/A): 0.6209230 object centre (A): -6.920000 0.1735001 16.02900 number of atom coordinates read : 2583 total number of charged atoms : 2450 net assigned charge : 3.906009 assigned positive charge : 393.0441 centred at (gu) : 88.49699 88.86454 89.87445 assigned negative charge : -389.1385 centred at (gu) : 88.39803 88.91115 89.75484 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6493 nv = 96 ne = 84 npr = 54035 no. pairs analyzed = 54035 no. exposed pairs = 2968 no. arc points = 21320 no. surface atoms = 1002 nbur = 1581 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 337 mr = 3670 m= 0 mr = 38 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 31 time to turn everything in is 0.3000000 number of dielectric boundary points 3122 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2128 ## 220 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8035 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.0958495E-09 1.1054018E-08 midg,1,midg; midg,igrid,midg 8.3161620E-09 1.2862350E-10 1,midg,midg; igrid,midg,midg -5.0106030E-09 7.1953132E-09 gauss-seidel spectral radius is 0.9865618 estimated iterations to convergence 71 setup time was (sec) 0.5400000 now iterating at: 19:46:17 rms-change max change #iterations 0.1297777 20.85595 at 10iterations 1.1900390E-02 1.767647 at 20iterations 1.1114776E-03 0.1774340 at 30iterations 1.0119700E-04 1.3702393E-02 at 40iterations 9.4586458E-06 1.3484955E-03 at 50iterations finished qdiffx linear iterations at : 19:46:19 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 9.4586458E-06 1.3484955E-03 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 19:46:20 3.385u 0.205s 0:03.85 92.9% 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 Sat Oct 8 2011 at 19:46:20 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: 295 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: ZN5 547 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.862769 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): -31.52500 17.68500 ymin,ymax (A): -23.34500 23.69200 zmin,zma (A): -12.63800 44.69600 x,y,z range (A): 49.21000 47.03700 57.33400 scale (grids/A): 1.862769 object centre (A): -6.920000 0.1735001 16.02900 number of atom coordinates read : 2583 total number of charged atoms : 2450 net assigned charge : 3.906009 assigned positive charge : 393.0441 centred at (gu) : 85.49042 86.59328 89.62300 assigned negative charge : -389.1385 centred at (gu) : 85.19402 86.73315 89.26423 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 70613 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21320 grid for indexing accessible points = 1.400000 m= 24492 mr = 49512 m= 3550 mr = 18160 m= 200 mr = 2260 m= 0 mr = 69 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 3314 time to turn everything in is 0.5000000 number of dielectric boundary points 28854 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 166 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 19214 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) : 0.6209230 object centre at (A) : -6.920000 0.1735001 16.02900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7410802E-02 3.2845788E-02 midg,1,midg; midg,igrid,midg 1.4029282E-02 2.3879248E-03 1,midg,midg; igrid,midg,midg -5.7334201E-03 3.0718090E-02 gauss-seidel spectral radius is 0.9985669 estimated iterations to convergence 209 setup time was (sec) 0.8000000 now iterating at: 19:46:21 rms-change max change #iterations 4.057136 195.6685 at 10iterations 1.867590 63.54324 at 20iterations 0.8567519 27.53784 at 30iterations 0.3930230 13.92265 at 40iterations 0.1814086 5.500702 at 50iterations 8.3262682E-02 2.607918 at 60iterations 3.8456466E-02 1.228592 at 70iterations 1.7658150E-02 0.6035881 at 80iterations 8.1148297E-03 0.2865553 at 90iterations 3.7264742E-03 0.1167717 at 100iterations 1.7188903E-03 5.5549622E-02 at 110iterations 7.8933820E-04 2.8318405E-02 at 120iterations finished qdiffx linear iterations at : 19:46:27 total time elapsed so far: 7.490000 # loops : 120 mean,max change (kT/e) : 7.8933820E-04 2.8318405E-02 energy calculations done at 7.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.660000 DelPhi exited at 19:46:28 7.666u 0.242s 0:08.19 96.4% 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 19:46:28 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: 295 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: ZN5 547 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.794153 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): -31.52500 17.68500 ymin,ymax (A): -23.34500 23.69200 zmin,zma (A): -12.63800 44.69600 x,y,z range (A): 49.21000 47.03700 57.33400 scale (grids/A): 2.794153 object centre (A): -6.920000 0.1735001 16.02900 number of atom coordinates read : 2583 total number of charged atoms : 2450 net assigned charge : 3.906009 assigned positive charge : 393.0441 centred at (gu) : 83.23538 84.88980 89.43444 assigned negative charge : -389.1385 centred at (gu) : 82.79101 85.09965 88.89622 start vw surface at 0.1600000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 163327 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21320 grid for indexing accessible points = 1.400000 m= 80749 mr = 119701 m= 27459 mr = 66575 m= 6387 mr = 22106 m= 812 mr = 4907 m= 40 mr = 551 m= 0 mr = 9 time to grow re-entrant surface = 0.6900000 no. cavity mid-points inaccessible to solvent = 11757 time to turn everything in is 1.250000 number of dielectric boundary points 64925 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.390000 number of grid points assigned charge 19598 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) : 1.862769 object centre at (A) : -6.920000 0.1735001 16.02900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.7321144E-02 0.3771041 midg,1,midg; midg,igrid,midg 0.1611082 5.6486931E-03 1,midg,midg; igrid,midg,midg -2.3027562E-02 0.3860571 gauss-seidel spectral radius is 0.9992329 estimated iterations to convergence 285 setup time was (sec) 1.560000 now iterating at: 19:46:30 rms-change max change #iterations 9.531523 288.6517 at 10iterations 5.462740 113.7387 at 20iterations 3.115817 67.73186 at 30iterations 1.773806 34.02893 at 40iterations 1.006855 19.61629 at 50iterations 0.5717757 11.97636 at 60iterations 0.3255813 5.902554 at 70iterations 0.1847755 3.263597 at 80iterations 0.1053100 2.022676 at 90iterations 5.9628624E-02 1.177092 at 100iterations 3.3891927E-02 0.6409721 at 110iterations 1.9277379E-02 0.3342657 at 120iterations 1.0932282E-02 0.1899228 at 130iterations 6.2127239E-03 0.1204586 at 140iterations 3.5302574E-03 6.5416813E-02 at 150iterations 2.0038337E-03 3.6785126E-02 at 160iterations 1.1381861E-03 2.0223618E-02 at 170iterations 6.4667908E-04 1.2247086E-02 at 180iterations finished qdiffx linear iterations at : 19:46:41 total time elapsed so far: 12.26000 # loops : 180 mean,max change (kT/e) : 6.4667908E-04 1.2247086E-02 energy calculations done at 12.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.44000 DelPhi exited at 19:46:41 12.438u 0.251s 0:12.95 97.9% 0+0k 0+0io 0pf+0w