Tue Oct 11 06:01:13 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 06:01:13 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 = 2318 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 0.7060130 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): 25.68500 72.99700 ymin,ymax (A): -18.74800 31.67600 zmin,zma (A): 3.821000 46.19600 x,y,z range (A): 47.31200 50.42400 42.37500 scale (grids/A): 0.7060130 object centre (A): 49.34100 6.464001 25.00850 number of atom coordinates read : 2318 total number of charged atoms : 1988 net assigned charge : 5.945011 assigned positive charge : 325.3760 centred at (gu) : 88.85687 90.14857 90.36197 assigned negative charge : -319.4310 centred at (gu) : 88.98284 90.08975 90.44656 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7131 nv = 96 ne = 84 npr = 42571 no. pairs analyzed = 42571 no. exposed pairs = 2570 no. arc points = 17322 no. surface atoms = 876 nbur = 1442 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 457 mr = 4107 m= 4 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3410 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1609 ## 156 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7893 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.2925496E-08 6.2639600E-09 midg,1,midg; midg,igrid,midg 1.8378969E-08 7.8705106E-08 1,midg,midg; igrid,midg,midg 1.3612784E-07 -1.1159203E-08 gauss-seidel spectral radius is 0.9895449 estimated iterations to convergence 80 setup time was (sec) 0.3500000 now iterating at: 06:01:14 rms-change max change #iterations 0.2069862 27.45384 at 10iterations 2.5671253E-02 3.675629 at 20iterations 3.5432228E-03 0.6369781 at 30iterations 6.2981015E-04 7.5300217E-02 at 40iterations 1.6877028E-04 2.0324707E-02 at 50iterations finished qdiffx linear iterations at : 06:01:17 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 1.6877028E-04 2.0324707E-02 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 06:01:17 3.303u 0.169s 0:03.78 91.5% 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 06:01:17 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 = 2318 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 2.118039 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): 25.68500 72.99700 ymin,ymax (A): -18.74800 31.67600 zmin,zma (A): 3.821000 46.19600 x,y,z range (A): 47.31200 50.42400 42.37500 scale (grids/A): 2.118039 object centre (A): 49.34100 6.464001 25.00850 number of atom coordinates read : 2318 total number of charged atoms : 1988 net assigned charge : 5.945011 assigned positive charge : 325.3760 centred at (gu) : 86.57048 90.44566 91.08614 assigned negative charge : -319.4310 centred at (gu) : 86.94847 90.26918 91.33978 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 75819 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17322 grid for indexing accessible points = 1.400000 m= 30903 mr = 54179 m= 5865 mr = 23564 m= 547 mr = 3912 m= 18 mr = 270 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 31227 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 65 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 15761 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) : 0.7060130 object centre at (A) : 49.34100 6.464001 25.00850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9628361E-02 2.5449106E-02 midg,1,midg; midg,igrid,midg 4.1969344E-02 2.7764639E-02 1,midg,midg; igrid,midg,midg 4.5677863E-02 -3.9528154E-02 gauss-seidel spectral radius is 0.9988286 estimated iterations to convergence 231 setup time was (sec) 0.6000000 now iterating at: 06:01:18 rms-change max change #iterations 4.648682 175.8892 at 10iterations 2.301579 79.63046 at 20iterations 1.143405 36.31573 at 30iterations 0.5656641 18.01335 at 40iterations 0.2807911 8.515512 at 50iterations 0.1395400 4.197802 at 60iterations 6.9302529E-02 2.037830 at 70iterations 3.4546286E-02 1.085036 at 80iterations 1.7215991E-02 0.5938587 at 90iterations 8.6504528E-03 0.2566013 at 100iterations 4.3813828E-03 0.1347980 at 110iterations 2.2610156E-03 7.4697495E-02 at 120iterations finished qdiffx linear iterations at : 06:01:25 total time elapsed so far: 7.550000 # loops : 120 mean,max change (kT/e) : 2.2610156E-03 7.4697495E-02 energy calculations done at 7.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.690000 DelPhi exited at 06:01:26 7.690u 0.182s 0:08.50 92.5% 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 06:01:26 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 = 2318 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 3.177058 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): 25.68500 72.99700 ymin,ymax (A): -18.74800 31.67600 zmin,zma (A): 3.821000 46.19600 x,y,z range (A): 47.31200 50.42400 42.37500 scale (grids/A): 3.177058 object centre (A): 49.34100 6.464001 25.00850 number of atom coordinates read : 2318 total number of charged atoms : 1988 net assigned charge : 5.945011 assigned positive charge : 325.3760 centred at (gu) : 84.85565 90.66851 91.62921 assigned negative charge : -319.4310 centred at (gu) : 85.42269 90.40379 92.00959 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 175060 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17322 grid for indexing accessible points = 1.400000 m= 96025 mr = 130639 m= 39093 mr = 80150 m= 11092 mr = 32311 m= 2216 mr = 8573 m= 270 mr = 1565 m= 19 mr = 185 m= 0 mr = 5 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.160000 number of dielectric boundary points 70347 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.240000 number of grid points assigned charge 15903 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) : 2.118039 object centre at (A) : 49.34100 6.464001 25.00850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1132966 0.2147742 midg,1,midg; midg,igrid,midg 0.3581382 0.1231622 1,midg,midg; igrid,midg,midg 0.4786023 -0.4569890 gauss-seidel spectral radius is 0.9992971 estimated iterations to convergence 298 setup time was (sec) 1.380000 now iterating at: 06:01:27 rms-change max change #iterations 10.36699 395.1503 at 10iterations 6.147835 173.9890 at 20iterations 3.637892 82.73137 at 30iterations 2.141852 42.60952 at 40iterations 1.260000 23.70160 at 50iterations 0.7428102 15.10128 at 60iterations 0.4357325 7.347065 at 70iterations 0.2552496 4.336357 at 80iterations 0.1499320 2.578507 at 90iterations 8.7935224E-02 1.813772 at 100iterations 5.1833346E-02 0.8348732 at 110iterations 3.0557353E-02 0.5162354 at 120iterations 1.8193847E-02 0.3283730 at 130iterations 1.0991363E-02 0.1919022 at 140iterations 6.8119848E-03 0.1394577 at 150iterations 4.3624635E-03 8.1420898E-02 at 160iterations 2.9599611E-03 6.0291290E-02 at 170iterations 2.1203498E-03 4.0443420E-02 at 180iterations finished qdiffx linear iterations at : 06:01:38 total time elapsed so far: 12.46000 # loops : 180 mean,max change (kT/e) : 2.1203498E-03 4.0443420E-02 energy calculations done at 12.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.60000 DelPhi exited at 06:01:39 12.598u 0.216s 0:13.21 96.8% 0+0k 0+0io 0pf+0w