Tue Nov 22 14:12:11 PST 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 Nov 22 2011 at 14:12:16 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 = 1958 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: 0.5992560 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): -35.02900 10.39000 ymin,ymax (A): 0.2630000 41.60600 zmin,zma (A): -0.4560000 58.95100 x,y,z range (A): 45.41900 41.34300 59.40700 scale (grids/A): 0.5992560 object centre (A): -12.31950 20.93450 29.24750 number of atom coordinates read : 1958 total number of charged atoms : 1826 net assigned charge : 5.000007 assigned positive charge : 291.4219 centred at (gu) : 90.25800 89.63863 89.19791 assigned negative charge : -286.4223 centred at (gu) : 90.24443 89.71077 89.19318 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 4646 nv = 96 ne = 84 npr = 40550 no. pairs analyzed = 40550 no. exposed pairs = 2435 no. arc points = 17013 no. surface atoms = 822 nbur = 1136 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 227 mr = 2541 m= 1 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 2300 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1682 ## 192 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 5714 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3363449E-09 1.8511945E-09 midg,1,midg; midg,igrid,midg 4.3022506E-09 1.6372653E-10 1,midg,midg; igrid,midg,midg 1.6313088E-09 2.5831512E-09 gauss-seidel spectral radius is 0.9855314 estimated iterations to convergence 68 setup time was (sec) 0.4300000 now iterating at: 14:12:20 rms-change max change #iterations 9.2735447E-02 15.86191 at 10iterations 7.8058401E-03 1.478642 at 20iterations 6.7144883E-04 0.1161575 at 30iterations 5.5258839E-05 9.2651844E-03 at 40iterations 4.7278186E-06 9.9182129E-04 at 50iterations finished qdiffx linear iterations at : 14:12:28 total time elapsed so far: 2.870000 # loops : 50 mean,max change (kT/e) : 4.7278186E-06 9.9182129E-04 energy calculations done at 2.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.040000 DelPhi exited at 14:12:30 3.048u 0.137s 0:14.19 22.3% 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 Nov 22 2011 at 14:12:35 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 = 1958 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: 1.797768 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): -35.02900 10.39000 ymin,ymax (A): 0.2630000 41.60600 zmin,zma (A): -0.4560000 58.95100 x,y,z range (A): 45.41900 41.34300 59.40700 scale (grids/A): 1.797768 object centre (A): -12.31950 20.93450 29.24750 number of atom coordinates read : 1958 total number of charged atoms : 1826 net assigned charge : 5.000007 assigned positive charge : 291.4219 centred at (gu) : 90.77399 88.91573 87.59348 assigned negative charge : -286.4223 centred at (gu) : 90.73368 89.13277 87.57968 start vw surface at 0.1200000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 50363 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17013 grid for indexing accessible points = 1.400000 m= 17451 mr = 34453 m= 2448 mr = 12977 m= 130 mr = 1601 m= 0 mr = 60 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 550 time to turn everything in is 0.3700000 number of dielectric boundary points 21301 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 126 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 14241 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) : 0.5992560 object centre at (A) : -12.31950 20.93450 29.24750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2929667E-02 2.7190270E-02 midg,1,midg; midg,igrid,midg 3.3945267E-03 2.0842871E-03 1,midg,midg; igrid,midg,midg 7.3353335E-04 -2.2136294E-03 gauss-seidel spectral radius is 0.9983889 estimated iterations to convergence 198 setup time was (sec) 0.6600000 now iterating at: 14:12:40 rms-change max change #iterations 3.192126 160.7967 at 10iterations 1.396428 59.37010 at 20iterations 0.6130542 22.18285 at 30iterations 0.2695684 10.51713 at 40iterations 0.1172453 4.341770 at 50iterations 5.1798198E-02 1.852562 at 60iterations 2.2687342E-02 0.9528198 at 70iterations 9.9397060E-03 0.3875370 at 80iterations 4.3691001E-03 0.1798248 at 90iterations 1.9016615E-03 7.5898886E-02 at 100iterations 8.3614310E-04 3.2470703E-02 at 110iterations 3.6833482E-04 1.4187574E-02 at 120iterations finished qdiffx linear iterations at : 14:12:59 total time elapsed so far: 6.830000 # loops : 120 mean,max change (kT/e) : 3.6833482E-04 1.4187574E-02 energy calculations done at 6.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.000000 DelPhi exited at 14:13:03 7.003u 0.183s 0:28.91 24.8% 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 Tue Nov 22 2011 at 14:13:05 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 = 1958 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: 2.696652 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): -35.02900 10.39000 ymin,ymax (A): 0.2630000 41.60600 zmin,zma (A): -0.4560000 58.95100 x,y,z range (A): 45.41900 41.34300 59.40700 scale (grids/A): 2.696652 object centre (A): -12.31950 20.93450 29.24750 number of atom coordinates read : 1958 total number of charged atoms : 1826 net assigned charge : 5.000007 assigned positive charge : 291.4219 centred at (gu) : 91.16090 88.37359 86.39028 assigned negative charge : -286.4223 centred at (gu) : 91.10056 88.69920 86.36958 start vw surface at 0.1000000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 116320 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17013 grid for indexing accessible points = 1.400000 m= 57708 mr = 83257 m= 19723 mr = 47327 m= 4304 mr = 16090 m= 544 mr = 3380 m= 38 mr = 403 m= 0 mr = 15 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 1760 time to turn everything in is 0.8700000 number of dielectric boundary points 48165 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 14605 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) : 1.797768 object centre at (A) : -12.31950 20.93450 29.24750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1111636 0.2947525 midg,1,midg; midg,igrid,midg 4.8803878E-03 1.6658137E-02 1,midg,midg; igrid,midg,midg -1.7975980E-02 -5.1949590E-02 gauss-seidel spectral radius is 0.9991698 estimated iterations to convergence 274 setup time was (sec) 1.140000 now iterating at: 14:13:13 rms-change max change #iterations 7.732853 367.1868 at 10iterations 4.331261 108.1888 at 20iterations 2.420801 57.19170 at 30iterations 1.350540 30.43614 at 40iterations 0.7494702 18.04030 at 50iterations 0.4151104 9.030602 at 60iterations 0.2308939 5.292946 at 70iterations 0.1278305 2.696384 at 80iterations 7.0807233E-02 1.627600 at 90iterations 3.9215889E-02 0.8205123 at 100iterations 2.1820599E-02 0.5316448 at 110iterations 1.2068087E-02 0.2703457 at 120iterations 6.6960035E-03 0.1421399 at 130iterations 3.7060271E-03 7.9864502E-02 at 140iterations 2.0580995E-03 4.5166016E-02 at 150iterations 1.1410144E-03 2.5002837E-02 at 160iterations 6.3344545E-04 1.4955521E-02 at 170iterations 3.5124368E-04 7.6618195E-03 at 180iterations finished qdiffx linear iterations at : 14:13:43 total time elapsed so far: 11.05000 # loops : 180 mean,max change (kT/e) : 3.5124368E-04 7.6618195E-03 energy calculations done at 11.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.22000 DelPhi exited at 14:13:46 11.219u 0.199s 0:41.24 27.6% 0+0k 0+0io 0pf+0w