Wed Feb 1 01:22:27 PST 2012 #!/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 Wed Feb 1 2012 at 01:22:27 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 ! Automatically converted by prot2crg.py # of charge parameter records: 337 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2028 !!! WARNING: DIC 140 has a net charge of -0.8000 !!! WARNING: DIC 168 has a net charge of -0.8000 !!! WARNING: ASZ 169 has a net charge of 0.1000 !!! WARNING: MG 215 has a net charge of 1.4000 !!! WARNING: WAM 901 has a net charge of 0.1000 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: 0.7222853 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): -32.36100 16.92700 ymin,ymax (A): -31.40900 17.59000 zmin,zma (A): -35.75900 9.563000 x,y,z range (A): 49.28800 48.99900 45.32200 scale (grids/A): 0.7222853 object centre (A): -7.717000 -6.909500 -13.09800 number of atom coordinates read : 2028 total number of charged atoms : 1952 net assigned charge : -4.999983 assigned positive charge : 315.1888 centred at (gu) : 88.95547 90.29200 92.09474 assigned negative charge : -320.1891 centred at (gu) : 88.93317 90.32343 92.07211 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7475 nv = 96 ne = 84 npr = 41139 no. pairs analyzed = 41139 no. exposed pairs = 2304 no. arc points = 16402 no. surface atoms = 778 nbur = 1250 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 537 mr = 4606 m= 5 mr = 132 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 265 time to turn everything in is 0.1800000 number of dielectric boundary points 3279 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1263 ## 82 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 7965 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.1058606E-08 -6.3738504E-08 midg,1,midg; midg,igrid,midg -3.5537852E-08 -8.5881140E-08 1,midg,midg; igrid,midg,midg -9.1141999E-08 -3.6294967E-08 gauss-seidel spectral radius is 0.9900028 estimated iterations to convergence 81 setup time was (sec) 0.3700000 now iterating at: 01:22:28 rms-change max change #iterations 0.2253510 30.44036 at 10iterations 2.9198823E-02 3.900197 at 20iterations 3.7514677E-03 0.4626904 at 30iterations 4.7864002E-04 5.8151245E-02 at 40iterations 6.2390442E-05 8.9044571E-03 at 50iterations finished qdiffx linear iterations at : 01:22:31 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 6.2390442E-05 8.9044571E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 01:22:31 3.398u 0.183s 0:03.86 92.4% 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 Wed Feb 1 2012 at 01:22:31 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 ! Automatically converted by prot2crg.py # of charge parameter records: 337 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2028 !!! WARNING: DIC 140 has a net charge of -0.8000 !!! WARNING: DIC 168 has a net charge of -0.8000 !!! WARNING: ASZ 169 has a net charge of 0.1000 !!! WARNING: MG 215 has a net charge of 1.4000 !!! WARNING: WAM 901 has a net charge of 0.1000 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: 2.166856 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): -32.36100 16.92700 ymin,ymax (A): -31.40900 17.59000 zmin,zma (A): -35.75900 9.563000 x,y,z range (A): 49.28800 48.99900 45.32200 scale (grids/A): 2.166856 object centre (A): -7.717000 -6.909500 -13.09800 number of atom coordinates read : 2028 total number of charged atoms : 1952 net assigned charge : -4.999983 assigned positive charge : 315.1888 centred at (gu) : 86.86637 90.87574 96.28387 assigned negative charge : -320.1891 centred at (gu) : 86.79958 90.97025 96.21639 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 79465 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16402 grid for indexing accessible points = 1.400000 m= 33655 mr = 58177 m= 7371 mr = 27013 m= 762 mr = 5469 m= 17 mr = 530 m= 0 mr = 2 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 6735 time to turn everything in is 0.4100000 number of dielectric boundary points 30079 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 35 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 15529 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) : 0.7222853 object centre at (A) : -7.717000 -6.909500 -13.09800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.8297028E-03 -3.0814396E-02 midg,1,midg; midg,igrid,midg -4.4254921E-02 -2.6181100E-02 1,midg,midg; igrid,midg,midg -4.5684345E-02 -3.1446215E-02 gauss-seidel spectral radius is 0.9988641 estimated iterations to convergence 235 setup time was (sec) 0.6400000 now iterating at: 01:22:32 rms-change max change #iterations 4.878843 221.9815 at 10iterations 2.433253 82.02302 at 20iterations 1.224901 40.36159 at 30iterations 0.6136714 18.87798 at 40iterations 0.3080626 8.978810 at 50iterations 0.1538586 4.876755 at 60iterations 7.7272303E-02 2.249130 at 70iterations 3.8635809E-02 1.311776 at 80iterations 1.9429520E-02 0.5763397 at 90iterations 9.7129764E-03 0.3058052 at 100iterations 4.8827399E-03 0.1387558 at 110iterations 2.4447928E-03 7.3074341E-02 at 120iterations finished qdiffx linear iterations at : 01:22:39 total time elapsed so far: 7.840000 # loops : 120 mean,max change (kT/e) : 2.4447928E-03 7.3074341E-02 energy calculations done at 7.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.980000 DelPhi exited at 01:22:40 7.981u 0.298s 0:08.54 96.8% 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 Wed Feb 1 2012 at 01:22:40 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 ! Automatically converted by prot2crg.py # of charge parameter records: 337 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2028 !!! WARNING: DIC 140 has a net charge of -0.8000 !!! WARNING: DIC 168 has a net charge of -0.8000 !!! WARNING: ASZ 169 has a net charge of 0.1000 !!! WARNING: MG 215 has a net charge of 1.4000 !!! WARNING: WAM 901 has a net charge of 0.1000 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: 3.250284 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): -32.36100 16.92700 ymin,ymax (A): -31.40900 17.59000 zmin,zma (A): -35.75900 9.563000 x,y,z range (A): 49.28800 48.99900 45.32200 scale (grids/A): 3.250284 object centre (A): -7.717000 -6.909500 -13.09800 number of atom coordinates read : 2028 total number of charged atoms : 1952 net assigned charge : -4.999983 assigned positive charge : 315.1888 centred at (gu) : 85.29945 91.31367 99.42571 assigned negative charge : -320.1891 centred at (gu) : 85.19939 91.45542 99.32465 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 183283 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16402 grid for indexing accessible points = 1.400000 m= 102736 mr = 139348 m= 45337 mr = 88202 m= 14366 mr = 39111 m= 3235 mr = 12024 m= 466 mr = 2615 m= 13 mr = 353 m= 0 mr = 0 time to grow re-entrant surface = 0.6200001 no. cavity mid-points inaccessible to solvent = 22772 time to turn everything in is 1.220000 number of dielectric boundary points 67783 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 15616 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) : 2.166856 object centre at (A) : -7.717000 -6.909500 -13.09800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3855258E-02 -0.4276074 midg,1,midg; midg,igrid,midg -0.7157820 -0.2833790 1,midg,midg; igrid,midg,midg -0.3272642 -0.2963762 gauss-seidel spectral radius is 0.9993029 estimated iterations to convergence 299 setup time was (sec) 1.470000 now iterating at: 01:22:42 rms-change max change #iterations 10.67736 390.7419 at 10iterations 6.263706 118.8987 at 20iterations 3.670346 70.66747 at 30iterations 2.140040 37.33563 at 40iterations 1.252725 21.40371 at 50iterations 0.7335314 12.97660 at 60iterations 0.4277695 7.130750 at 70iterations 0.2498203 4.313940 at 80iterations 0.1457736 2.488849 at 90iterations 8.5239083E-02 1.418080 at 100iterations 4.9729798E-02 0.8490658 at 110iterations 2.9006531E-02 0.4514656 at 120iterations 1.6981347E-02 0.2779016 at 130iterations 9.9220816E-03 0.1623173 at 140iterations 5.7867523E-03 0.1029816 at 150iterations 3.3884421E-03 5.5465698E-02 at 160iterations 1.9758253E-03 3.5964966E-02 at 170iterations 1.1531707E-03 1.9371033E-02 at 180iterations finished qdiffx linear iterations at : 01:22:53 total time elapsed so far: 12.91000 # loops : 180 mean,max change (kT/e) : 1.1531707E-03 1.9371033E-02 energy calculations done at 12.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.04000 DelPhi exited at 01:22:54 13.045u 0.331s 0:13.66 97.8% 0+0k 0+0io 0pf+0w