Mon Oct 10 17:09:50 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+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 Mon Oct 10 2011 at 17:09:50 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2089 !!! WARNING: HIZ 66 has a net charge of 0.2000 !!! WARNING: HIZ 81 has a net charge of 0.2000 !!! WARNING: HIY 94 has a net charge of 0.2000 !!! WARNING: HIZ 116 has a net charge of 0.2000 !!! WARNING: HIZ 120 has a net charge of 0.2000 !!! WARNING: HIZ 126 has a net charge of 0.2000 !!! WARNING: HIZ 541 has a net charge of 0.2000 !!! WARNING: HIY 569 has a net charge of 0.2000 !!! WARNING: ZN6 632 has a net charge of 1.4000 !!! WARNING: ZN6 633 has a net charge of 1.4000 !!! WARNING: ZN6 639 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6611693 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): -7.815000 33.18000 ymin,ymax (A): 35.16100 88.96500 zmin,zma (A): 17.17000 71.01400 x,y,z range (A): 40.99500 53.80400 53.84400 scale (grids/A): 0.6611693 object centre (A): 12.68250 62.06300 44.09200 number of atom coordinates read : 2089 total number of charged atoms : 1960 net assigned charge : -1.699993 assigned positive charge : 301.8450 centred at (gu) : 89.21510 90.60985 89.02052 assigned negative charge : -303.5450 centred at (gu) : 89.21683 90.71837 88.76942 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6226 nv = 96 ne = 84 npr = 43135 no. pairs analyzed = 43135 no. exposed pairs = 2827 no. arc points = 20953 no. surface atoms = 938 nbur = 1151 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 349 mr = 3095 m= 3 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 42 time to turn everything in is 0.2700000 number of dielectric boundary points 3451 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1897 ## 153 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7151 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.5231716E-08 2.8491080E-08 midg,1,midg; midg,igrid,midg 1.1607214E-08 -2.4208207E-08 1,midg,midg; igrid,midg,midg -4.1543333E-09 -3.5128684E-09 gauss-seidel spectral radius is 0.9881070 estimated iterations to convergence 75 setup time was (sec) 0.5700000 now iterating at: 17:09:51 rms-change max change #iterations 0.1541322 25.99981 at 10iterations 1.6076520E-02 2.264722 at 20iterations 1.7289117E-03 0.2617874 at 30iterations 1.8761367E-04 3.2215118E-02 at 40iterations 2.0784884E-05 3.0665398E-03 at 50iterations finished qdiffx linear iterations at : 17:09:54 total time elapsed so far: 4.280000 # loops : 50 mean,max change (kT/e) : 2.0784884E-05 3.0665398E-03 energy calculations done at 4.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.460000 DelPhi exited at 17:09:55 4.463u 0.422s 0:05.17 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 Mon Oct 10 2011 at 17:09:55 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2089 !!! WARNING: HIZ 66 has a net charge of 0.2000 !!! WARNING: HIZ 81 has a net charge of 0.2000 !!! WARNING: HIY 94 has a net charge of 0.2000 !!! WARNING: HIZ 116 has a net charge of 0.2000 !!! WARNING: HIZ 120 has a net charge of 0.2000 !!! WARNING: HIZ 126 has a net charge of 0.2000 !!! WARNING: HIZ 541 has a net charge of 0.2000 !!! WARNING: HIY 569 has a net charge of 0.2000 !!! WARNING: ZN6 632 has a net charge of 1.4000 !!! WARNING: ZN6 633 has a net charge of 1.4000 !!! WARNING: ZN6 639 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.983508 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): -7.815000 33.18000 ymin,ymax (A): 35.16100 88.96500 zmin,zma (A): 17.17000 71.01400 x,y,z range (A): 40.99500 53.80400 53.84400 scale (grids/A): 1.983508 object centre (A): 12.68250 62.06300 44.09200 number of atom coordinates read : 2089 total number of charged atoms : 1960 net assigned charge : -1.699993 assigned positive charge : 301.8450 centred at (gu) : 87.64554 91.82928 87.06155 assigned negative charge : -303.5450 centred at (gu) : 87.65064 92.15506 86.30804 start vw surface at 0.1100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 65933 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20953 grid for indexing accessible points = 1.400000 m= 22294 mr = 42642 m= 3554 mr = 15493 m= 263 mr = 2054 m= 11 mr = 111 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 1362 time to turn everything in is 0.5600000 number of dielectric boundary points 31755 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 101 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 15514 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) : 0.6611693 object centre at (A) : 12.68250 62.06300 44.09200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.8366430E-02 5.7413470E-02 midg,1,midg; midg,igrid,midg 1.6254572E-02 -6.2915184E-02 1,midg,midg; igrid,midg,midg -7.8269193E-04 -2.0256275E-04 gauss-seidel spectral radius is 0.9987019 estimated iterations to convergence 220 setup time was (sec) 0.8600000 now iterating at: 17:09:56 rms-change max change #iterations 4.030661 172.1176 at 10iterations 1.914517 66.18441 at 20iterations 0.9060186 32.78857 at 30iterations 0.4322978 14.01114 at 40iterations 0.2048396 7.035580 at 50iterations 9.7720496E-02 3.344551 at 60iterations 4.6423644E-02 1.538990 at 70iterations 2.2130003E-02 0.7373635 at 80iterations 1.0581636E-02 0.3516283 at 90iterations 5.0362097E-03 0.1614189 at 100iterations 2.3965144E-03 7.7243805E-02 at 110iterations 1.1421074E-03 3.6652565E-02 at 120iterations finished qdiffx linear iterations at : 17:10:06 total time elapsed so far: 10.21000 # loops : 120 mean,max change (kT/e) : 1.1421074E-03 3.6652565E-02 energy calculations done at 10.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.38000 DelPhi exited at 17:10:06 10.386u 0.462s 0:11.36 95.4% 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 Mon Oct 10 2011 at 17:10:06 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2089 !!! WARNING: HIZ 66 has a net charge of 0.2000 !!! WARNING: HIZ 81 has a net charge of 0.2000 !!! WARNING: HIY 94 has a net charge of 0.2000 !!! WARNING: HIZ 116 has a net charge of 0.2000 !!! WARNING: HIZ 120 has a net charge of 0.2000 !!! WARNING: HIZ 126 has a net charge of 0.2000 !!! WARNING: HIZ 541 has a net charge of 0.2000 !!! WARNING: HIY 569 has a net charge of 0.2000 !!! WARNING: ZN6 632 has a net charge of 1.4000 !!! WARNING: ZN6 633 has a net charge of 1.4000 !!! WARNING: ZN6 639 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.975262 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): -7.815000 33.18000 ymin,ymax (A): 35.16100 88.96500 zmin,zma (A): 17.17000 71.01400 x,y,z range (A): 40.99500 53.80400 53.84400 scale (grids/A): 2.975262 object centre (A): 12.68250 62.06300 44.09200 number of atom coordinates read : 2089 total number of charged atoms : 1960 net assigned charge : -1.699993 assigned positive charge : 301.8450 centred at (gu) : 86.46824 92.74395 85.59245 assigned negative charge : -303.5450 centred at (gu) : 86.47589 93.23258 84.46209 start vw surface at 0.1000000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 152296 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20953 grid for indexing accessible points = 1.400000 m= 72268 mr = 104296 m= 25431 mr = 56579 m= 6216 mr = 19773 m= 1044 mr = 4392 m= 91 mr = 634 m= 3 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 4552 time to turn everything in is 1.440000 number of dielectric boundary points 71651 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.570000 number of grid points assigned charge 15680 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) : 1.983508 object centre at (A) : 12.68250 62.06300 44.09200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3688559 0.9829916 midg,1,midg; midg,igrid,midg 0.3152033 -0.6512524 1,midg,midg; igrid,midg,midg 6.0001095E-03 -2.0572126E-02 gauss-seidel spectral radius is 0.9992799 estimated iterations to convergence 294 setup time was (sec) 1.760000 now iterating at: 17:10:09 rms-change max change #iterations 9.397380 377.9125 at 10iterations 5.560618 124.4087 at 20iterations 3.276274 72.61147 at 30iterations 1.927849 41.16868 at 40iterations 1.123819 25.09967 at 50iterations 0.6574790 14.20663 at 60iterations 0.3821139 7.448728 at 70iterations 0.2223622 4.452488 at 80iterations 0.1296093 2.431256 at 90iterations 7.5315267E-02 1.541756 at 100iterations 4.3641407E-02 0.8796935 at 110iterations 2.5291905E-02 0.4985962 at 120iterations 1.4678803E-02 0.3070374 at 130iterations 8.5263830E-03 0.1696692 at 140iterations 4.9542319E-03 9.3971252E-02 at 150iterations 2.8770757E-03 5.5882454E-02 at 160iterations 1.6743388E-03 3.0933380E-02 at 170iterations 9.7784831E-04 1.9269943E-02 at 180iterations finished qdiffx linear iterations at : 17:10:24 total time elapsed so far: 17.39000 # loops : 180 mean,max change (kT/e) : 9.7784831E-04 1.9269943E-02 energy calculations done at 17.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.56000 DelPhi exited at 17:10:25 17.567u 0.493s 0:18.38 98.2% 0+0k 0+0io 0pf+0w