Tue Oct 11 07:49:50 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+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 07:49:50 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2770 !!! WARNING: HIQ 55 has a net charge of 0.5140 !!! WARNING: GLM 204 has a net charge of -0.0940 !!! WARNING: SEP 207 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6351132 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): -13.29500 42.75800 ymin,ymax (A): -21.69300 26.60900 zmin,zma (A): -11.65600 40.30400 x,y,z range (A): 56.05300 48.30200 51.96000 scale (grids/A): 0.6351132 object centre (A): 14.73150 2.457999 14.32400 number of atom coordinates read : 2770 total number of charged atoms : 2400 net assigned charge : 8.945013 assigned positive charge : 388.6611 centred at (gu) : 90.02113 88.33614 90.85553 assigned negative charge : -379.7167 centred at (gu) : 90.03429 88.30898 91.05976 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6695 nv = 96 ne = 84 npr = 51872 no. pairs analyzed = 51872 no. exposed pairs = 2956 no. arc points = 20400 no. surface atoms = 1008 nbur = 1762 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 333 mr = 3824 m= 0 mr = 46 time to grow re-entrant surface = 9.9999987E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3158 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2078 ## 237 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8086 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6127998E-08 -1.1291281E-08 midg,1,midg; midg,igrid,midg 1.2448740E-08 1.0058272E-08 1,midg,midg; igrid,midg,midg 1.2783589E-08 1.0269034E-08 gauss-seidel spectral radius is 0.9871443 estimated iterations to convergence 72 setup time was (sec) 0.3900000 now iterating at: 07:49:51 rms-change max change #iterations 0.1432764 20.69741 at 10iterations 1.4324750E-02 1.935523 at 20iterations 1.7281723E-03 0.2681427 at 30iterations 2.8742620E-04 4.1362762E-02 at 40iterations 6.1456711E-05 9.6626282E-03 at 50iterations finished qdiffx linear iterations at : 07:49:54 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 6.1456711E-05 9.6626282E-03 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 07:49:54 3.363u 0.167s 0:03.82 92.1% 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 Tue Oct 11 2011 at 07:49:54 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2770 !!! WARNING: HIQ 55 has a net charge of 0.5140 !!! WARNING: GLM 204 has a net charge of -0.0940 !!! WARNING: SEP 207 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.905340 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): -13.29500 42.75800 ymin,ymax (A): -21.69300 26.60900 zmin,zma (A): -11.65600 40.30400 x,y,z range (A): 56.05300 48.30200 51.96000 scale (grids/A): 1.905340 object centre (A): 14.73150 2.457999 14.32400 number of atom coordinates read : 2770 total number of charged atoms : 2400 net assigned charge : 8.945013 assigned positive charge : 388.6611 centred at (gu) : 90.06270 85.00806 92.56623 assigned negative charge : -379.7167 centred at (gu) : 90.10280 84.92691 93.17905 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 72654 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20400 grid for indexing accessible points = 1.400000 m= 26617 mr = 51515 m= 4011 mr = 20159 m= 252 mr = 2457 m= 4 mr = 98 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 649 time to turn everything in is 0.3700000 number of dielectric boundary points 29309 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 168 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 18814 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) : 0.6351132 object centre at (A) : 14.73150 2.457999 14.32400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.3559028E-02 -1.2655141E-02 midg,1,midg; midg,igrid,midg 1.2879720E-02 2.1591060E-02 1,midg,midg; igrid,midg,midg 2.2090916E-02 3.0234890E-02 gauss-seidel spectral radius is 0.9986203 estimated iterations to convergence 213 setup time was (sec) 0.5800000 now iterating at: 07:49:55 rms-change max change #iterations 4.181372 168.1011 at 10iterations 1.961499 71.17471 at 20iterations 0.9145219 31.55448 at 30iterations 0.4270555 13.32977 at 40iterations 0.2003600 7.383669 at 50iterations 9.3748525E-02 3.071669 at 60iterations 4.3851599E-02 1.322182 at 70iterations 2.0605408E-02 0.6782980 at 80iterations 9.7376378E-03 0.2995014 at 90iterations 4.6333596E-03 0.1521664 at 100iterations 2.2237513E-03 7.2116852E-02 at 110iterations 1.0959328E-03 3.5850525E-02 at 120iterations finished qdiffx linear iterations at : 07:50:02 total time elapsed so far: 7.580000 # loops : 120 mean,max change (kT/e) : 1.0959328E-03 3.5850525E-02 energy calculations done at 7.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.710000 DelPhi exited at 07:50:03 7.713u 0.195s 0:08.28 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 Tue Oct 11 2011 at 07:50:03 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2770 !!! WARNING: HIQ 55 has a net charge of 0.5140 !!! WARNING: GLM 204 has a net charge of -0.0940 !!! WARNING: SEP 207 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.858009 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): -13.29500 42.75800 ymin,ymax (A): -21.69300 26.60900 zmin,zma (A): -11.65600 40.30400 x,y,z range (A): 56.05300 48.30200 51.96000 scale (grids/A): 2.858009 object centre (A): 14.73150 2.457999 14.32400 number of atom coordinates read : 2770 total number of charged atoms : 2400 net assigned charge : 8.945013 assigned positive charge : 388.6611 centred at (gu) : 90.09409 82.51196 93.84901 assigned negative charge : -379.7167 centred at (gu) : 90.15421 82.39036 94.76839 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 167901 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20400 grid for indexing accessible points = 1.400000 m= 86813 mr = 124344 m= 30925 mr = 72252 m= 7004 mr = 25060 m= 1048 mr = 5247 m= 75 mr = 731 m= 3 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 2359 time to turn everything in is 0.9300000 number of dielectric boundary points 66103 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 19197 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) : 1.905340 object centre at (A) : 14.73150 2.457999 14.32400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6982575 -0.2310448 midg,1,midg; midg,igrid,midg 0.1012839 0.2512371 1,midg,midg; igrid,midg,midg 0.1429688 0.1585415 gauss-seidel spectral radius is 0.9992428 estimated iterations to convergence 287 setup time was (sec) 1.160000 now iterating at: 07:50:04 rms-change max change #iterations 9.707236 365.7051 at 10iterations 5.598893 122.2028 at 20iterations 3.212547 59.70971 at 30iterations 1.846001 39.37746 at 40iterations 1.055376 19.88281 at 50iterations 0.6044867 10.91228 at 60iterations 0.3457622 6.434090 at 70iterations 0.1973906 3.543995 at 80iterations 0.1129694 2.098206 at 90iterations 6.4507917E-02 1.290382 at 100iterations 3.6947332E-02 0.6526756 at 110iterations 2.1216923E-02 0.3923187 at 120iterations 1.2211499E-02 0.2218781 at 130iterations 7.0607592E-03 0.1277888 at 140iterations 4.1342266E-03 7.8406334E-02 at 150iterations 2.4706186E-03 4.6348572E-02 at 160iterations 1.5107150E-03 3.0097961E-02 at 170iterations 9.6306461E-04 2.0248413E-02 at 180iterations finished qdiffx linear iterations at : 07:50:15 total time elapsed so far: 12.33000 # loops : 180 mean,max change (kT/e) : 9.6306461E-04 2.0248413E-02 energy calculations done at 12.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.46000 DelPhi exited at 07:50:16 12.465u 0.212s 0:13.01 97.3% 0+0k 0+0io 0pf+0w