Sun Oct 9 23:19:55 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 Sun Oct 9 2011 at 23:19:55 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3224 !!! WARNING: GLM 300 has a net charge of -0.6000 !!! WARNING: HIZ 304 has a net charge of 0.2000 !!! WARNING: GLM 685 has a net charge of -0.6000 !!! WARNING: ZN7 781 has a net charge of 1.4000 !!! WARNING: ZN7 782 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5621260 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): 24.79500 77.83700 ymin,ymax (A): -5.824000 57.50700 zmin,zma (A): 15.18600 68.36900 x,y,z range (A): 53.04200 63.33100 53.18300 scale (grids/A): 0.5621260 object centre (A): 51.31600 25.84150 41.77750 number of atom coordinates read : 3224 total number of charged atoms : 3077 net assigned charge : 7.800014 assigned positive charge : 492.8026 centred at (gu) : 89.51667 89.72524 90.35585 assigned negative charge : -485.0041 centred at (gu) : 89.55724 89.78495 90.34754 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6724 nv = 96 ne = 84 npr = 62374 no. pairs analyzed = 62374 no. exposed pairs = 4426 no. arc points = 31652 no. surface atoms = 1464 nbur = 1760 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 296 mr = 3271 m= 2 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3734 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3269 ## 446 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 8781 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.2202799E-10 1.0880460E-09 midg,1,midg; midg,igrid,midg 1.7786194E-09 1.0374257E-10 1,midg,midg; igrid,midg,midg 1.5923234E-09 3.2499423E-10 gauss-seidel spectral radius is 0.9837039 estimated iterations to convergence 64 setup time was (sec) 0.6100000 now iterating at: 23:19:56 rms-change max change #iterations 8.9673355E-02 13.59023 at 10iterations 6.3306424E-03 1.110023 at 20iterations 4.6276941E-04 8.2199097E-02 at 30iterations 3.4186673E-05 5.4626465E-03 at 40iterations 2.9263790E-06 3.9672852E-04 at 50iterations finished qdiffx linear iterations at : 23:19:59 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 2.9263790E-06 3.9672852E-04 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 23:19:59 3.595u 0.187s 0:04.18 90.1% 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 Sun Oct 9 2011 at 23:20:00 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3224 !!! WARNING: GLM 300 has a net charge of -0.6000 !!! WARNING: HIZ 304 has a net charge of 0.2000 !!! WARNING: GLM 685 has a net charge of -0.6000 !!! WARNING: ZN7 781 has a net charge of 1.4000 !!! WARNING: ZN7 782 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.686378 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): 24.79500 77.83700 ymin,ymax (A): -5.824000 57.50700 zmin,zma (A): 15.18600 68.36900 x,y,z range (A): 53.04200 63.33100 53.18300 scale (grids/A): 1.686378 object centre (A): 51.31600 25.84150 41.77750 number of atom coordinates read : 3224 total number of charged atoms : 3077 net assigned charge : 7.800014 assigned positive charge : 492.8026 centred at (gu) : 88.54932 89.17481 91.06657 assigned negative charge : -485.0041 centred at (gu) : 88.67164 89.35442 91.04230 start vw surface at 0.1800000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 74027 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31652 grid for indexing accessible points = 1.400000 m= 23018 mr = 48352 m= 2657 mr = 15524 m= 91 mr = 1305 m= 0 mr = 4 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 136 time to turn everything in is 0.5900000 number of dielectric boundary points 34608 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 371 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 23763 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) : 0.5621260 object centre at (A) : 51.31600 25.84150 41.77750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.4546493E-05 2.0165804E-03 midg,1,midg; midg,igrid,midg 1.7785951E-02 1.8842105E-02 1,midg,midg; igrid,midg,midg 8.3903233E-03 3.0122814E-03 gauss-seidel spectral radius is 0.9983510 estimated iterations to convergence 195 setup time was (sec) 0.8900000 now iterating at: 23:20:01 rms-change max change #iterations 3.738559 163.5925 at 10iterations 1.610076 64.75175 at 20iterations 0.6988001 23.36224 at 30iterations 0.3015573 9.709177 at 40iterations 0.1310768 4.286360 at 50iterations 5.6760453E-02 2.028428 at 60iterations 2.4543680E-02 0.8062134 at 70iterations 1.0720221E-02 0.3584843 at 80iterations 4.6303342E-03 0.1669798 at 90iterations 2.0146016E-03 6.7284584E-02 at 100iterations 8.7257510E-04 2.9474258E-02 at 110iterations 3.8038284E-04 1.3092995E-02 at 120iterations finished qdiffx linear iterations at : 23:20:08 total time elapsed so far: 7.880000 # loops : 120 mean,max change (kT/e) : 3.8038284E-04 1.3092995E-02 energy calculations done at 7.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.070000 DelPhi exited at 23:20:08 8.076u 0.226s 0:08.65 95.8% 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 Sun Oct 9 2011 at 23:20:08 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3224 !!! WARNING: GLM 300 has a net charge of -0.6000 !!! WARNING: HIZ 304 has a net charge of 0.2000 !!! WARNING: GLM 685 has a net charge of -0.6000 !!! WARNING: ZN7 781 has a net charge of 1.4000 !!! WARNING: ZN7 782 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.529567 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): 24.79500 77.83700 ymin,ymax (A): -5.824000 57.50700 zmin,zma (A): 15.18600 68.36900 x,y,z range (A): 53.04200 63.33100 53.18300 scale (grids/A): 2.529567 object centre (A): 51.31600 25.84150 41.77750 number of atom coordinates read : 3224 total number of charged atoms : 3077 net assigned charge : 7.800014 assigned positive charge : 492.8026 centred at (gu) : 87.82374 88.76196 91.59977 assigned negative charge : -485.0041 centred at (gu) : 88.00739 89.03141 91.56335 start vw surface at 0.1600000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 171555 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31652 grid for indexing accessible points = 1.400000 m= 78504 mr = 118619 m= 23253 mr = 60867 m= 4247 mr = 17313 m= 359 mr = 2784 m= 8 mr = 189 m= 0 mr = 0 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 483 time to turn everything in is 1.350000 number of dielectric boundary points 78154 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 20 iepsmp to db, and charging done at 1.500000 number of grid points assigned charge 24600 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) : 1.686378 object centre at (A) : 51.31600 25.84150 41.77750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.0125355E-02 -3.4268033E-02 midg,1,midg; midg,igrid,midg 0.2509434 0.3119280 1,midg,midg; igrid,midg,midg 0.1407012 8.5917175E-02 gauss-seidel spectral radius is 0.9992078 estimated iterations to convergence 281 setup time was (sec) 1.680000 now iterating at: 23:20:10 rms-change max change #iterations 9.648571 331.9545 at 10iterations 5.624562 146.0774 at 20iterations 3.253114 80.75961 at 30iterations 1.863557 51.18853 at 40iterations 1.069093 24.83106 at 50iterations 0.6095027 13.19118 at 60iterations 0.3469808 6.971600 at 70iterations 0.1970658 4.166677 at 80iterations 0.1117896 2.560853 at 90iterations 6.3211218E-02 1.390096 at 100iterations 3.5770096E-02 0.7634716 at 110iterations 2.0228358E-02 0.3994646 at 120iterations 1.1432871E-02 0.2188191 at 130iterations 6.4661321E-03 0.1237905 at 140iterations 3.6523759E-03 7.8392975E-02 at 150iterations 2.0604709E-03 4.2666435E-02 at 160iterations 1.1609603E-03 2.2160769E-02 at 170iterations 6.5618841E-04 1.3592839E-02 at 180iterations finished qdiffx linear iterations at : 23:20:21 total time elapsed so far: 12.90000 # loops : 180 mean,max change (kT/e) : 6.5618841E-04 1.3592839E-02 energy calculations done at 12.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.10000 DelPhi exited at 23:20:22 13.102u 0.242s 0:13.65 97.7% 0+0k 0+0io 0pf+0w