Tue Oct 11 05:20:10 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 05:20:10 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2305 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 !!! WARNING: ZN6 650 has a net charge of 1.4000 !!! WARNING: ZN6 651 has a net charge of 1.4000 !!! WARNING: ZN6 652 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: 0.6898422 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): 15.69200 63.03500 ymin,ymax (A): -3.547000 33.92600 zmin,zma (A): 20.16900 71.77500 x,y,z range (A): 47.34300 37.47300 51.60600 scale (grids/A): 0.6898422 object centre (A): 39.36350 15.18950 45.97200 number of atom coordinates read : 2305 total number of charged atoms : 1977 net assigned charge : 9.831008 assigned positive charge : 324.5439 centred at (gu) : 91.41721 89.66862 89.21088 assigned negative charge : -314.7131 centred at (gu) : 91.51981 89.60896 89.09598 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6776 nv = 96 ne = 84 npr = 42274 no. pairs analyzed = 42274 no. exposed pairs = 2583 no. arc points = 17745 no. surface atoms = 879 nbur = 1426 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 445 mr = 3888 m= 1 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3274 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1718 ## 178 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7680 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8649001E-08 7.9463483E-08 midg,1,midg; midg,igrid,midg 3.7298726E-08 7.0057006E-08 1,midg,midg; igrid,midg,midg 6.7315447E-08 2.6292529E-08 gauss-seidel spectral radius is 0.9890537 estimated iterations to convergence 78 setup time was (sec) 0.5700000 now iterating at: 05:20:11 rms-change max change #iterations 0.1863322 27.49368 at 10iterations 2.1730080E-02 2.881886 at 20iterations 2.6804109E-03 0.3861427 at 30iterations 3.7625336E-04 4.6157837E-02 at 40iterations 7.6910444E-05 1.1798859E-02 at 50iterations finished qdiffx linear iterations at : 05:20:14 total time elapsed so far: 3.830000 # loops : 50 mean,max change (kT/e) : 7.6910444E-05 1.1798859E-02 energy calculations done at 3.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.000000 DelPhi exited at 05:20:15 3.999u 0.277s 0:04.83 88.1% 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 05:20:15 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2305 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 !!! WARNING: ZN6 650 has a net charge of 1.4000 !!! WARNING: ZN6 651 has a net charge of 1.4000 !!! WARNING: ZN6 652 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: 2.069527 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): 15.69200 63.03500 ymin,ymax (A): -3.547000 33.92600 zmin,zma (A): 20.16900 71.77500 x,y,z range (A): 47.34300 37.47300 51.60600 scale (grids/A): 2.069527 object centre (A): 39.36350 15.18950 45.97200 number of atom coordinates read : 2305 total number of charged atoms : 1977 net assigned charge : 9.831008 assigned positive charge : 324.5439 centred at (gu) : 94.25188 89.00579 87.63267 assigned negative charge : -314.7131 centred at (gu) : 94.55942 88.82681 87.28800 start vw surface at 0.1600000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 72084 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17745 grid for indexing accessible points = 1.400000 m= 28667 mr = 51055 m= 5365 mr = 21742 m= 427 mr = 3514 m= 5 mr = 186 m= 0 mr = 2 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6800000 number of dielectric boundary points 30049 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 97 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 15677 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) : 0.6898422 object centre at (A) : 39.36350 15.18950 45.97200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2597100E-02 5.6066327E-02 midg,1,midg; midg,igrid,midg 2.6813582E-02 4.2512018E-02 1,midg,midg; igrid,midg,midg 2.5768608E-02 2.5305284E-02 gauss-seidel spectral radius is 0.9987803 estimated iterations to convergence 227 setup time was (sec) 0.9800000 now iterating at: 05:20:16 rms-change max change #iterations 4.489110 196.6920 at 10iterations 2.203448 71.48730 at 20iterations 1.070568 34.07365 at 30iterations 0.5245465 19.33885 at 40iterations 0.2563876 8.470241 at 50iterations 0.1258199 3.573214 at 60iterations 6.1376564E-02 1.855309 at 70iterations 3.0071167E-02 0.8966770 at 80iterations 1.4756052E-02 0.4593220 at 90iterations 7.2198552E-03 0.2424717 at 100iterations 3.5450798E-03 0.1061592 at 110iterations 1.7485436E-03 5.7001114E-02 at 120iterations finished qdiffx linear iterations at : 05:20:24 total time elapsed so far: 9.190000 # loops : 120 mean,max change (kT/e) : 1.7485436E-03 5.7001114E-02 energy calculations done at 9.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.370000 DelPhi exited at 05:20:25 9.371u 0.281s 0:10.22 94.4% 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 05:20:25 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2305 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 !!! WARNING: ZN6 650 has a net charge of 1.4000 !!! WARNING: ZN6 651 has a net charge of 1.4000 !!! WARNING: ZN6 652 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: 3.104290 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): 15.69200 63.03500 ymin,ymax (A): -3.547000 33.92600 zmin,zma (A): 20.16900 71.77500 x,y,z range (A): 47.34300 37.47300 51.60600 scale (grids/A): 3.104290 object centre (A): 39.36350 15.18950 45.97200 number of atom coordinates read : 2305 total number of charged atoms : 1977 net assigned charge : 9.831008 assigned positive charge : 324.5439 centred at (gu) : 96.37789 88.50858 86.44897 assigned negative charge : -314.7131 centred at (gu) : 96.83916 88.24034 85.93201 start vw surface at 0.1500000 fill in re-entrant regions at 0.9500000 boundary points on vw surface= 166282 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17745 grid for indexing accessible points = 1.400000 m= 89743 mr = 123060 m= 35851 mr = 74647 m= 9942 mr = 29375 m= 1844 mr = 7665 m= 174 mr = 1335 m= 3 mr = 98 m= 0 mr = 0 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.130000 number of dielectric boundary points 67659 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.290000 number of grid points assigned charge 15816 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) : 2.069527 object centre at (A) : 39.36350 15.18950 45.97200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4482379 0.4410644 midg,1,midg; midg,igrid,midg 0.2461815 0.3832763 1,midg,midg; igrid,midg,midg 0.2117488 0.4786457 gauss-seidel spectral radius is 0.9992845 estimated iterations to convergence 295 setup time was (sec) 2.460000 now iterating at: 05:20:28 rms-change max change #iterations 10.12393 415.4733 at 10iterations 5.962366 176.3557 at 20iterations 3.507876 87.28832 at 30iterations 2.056939 40.45807 at 40iterations 1.204762 23.86876 at 50iterations 0.7054949 14.49986 at 60iterations 0.4119082 7.945544 at 70iterations 0.2405535 4.635850 at 80iterations 0.1403765 2.524696 at 90iterations 8.1739634E-02 1.451853 at 100iterations 4.7785129E-02 0.9589424 at 110iterations 2.7879603E-02 0.5286913 at 120iterations 1.6304499E-02 0.3052979 at 130iterations 9.5706498E-03 0.1757722 at 140iterations 5.6693070E-03 9.8464966E-02 at 150iterations 3.3990981E-03 6.0989380E-02 at 160iterations 2.0913638E-03 4.2293549E-02 at 170iterations 1.3308442E-03 2.5638580E-02 at 180iterations finished qdiffx linear iterations at : 05:20:41 total time elapsed so far: 15.93000 # loops : 180 mean,max change (kT/e) : 1.3308442E-03 2.5638580E-02 energy calculations done at 15.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.10000 DelPhi exited at 05:20:42 16.105u 0.305s 0:16.74 97.9% 0+0k 0+0io 0pf+0w