Tue Oct 11 04:25:37 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 04:25:37 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: 331 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3002 !!! WARNING: HIR 43 has a net charge of 0.5140 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: 0.6499790 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): -10.46100 37.47400 ymin,ymax (A): -25.90100 22.31500 zmin,zma (A): -8.831000 45.94000 x,y,z range (A): 47.93500 48.21600 54.77100 scale (grids/A): 0.6499790 object centre (A): 13.50650 -1.792999 18.55450 number of atom coordinates read : 3002 total number of charged atoms : 2611 net assigned charge : 3.514024 assigned positive charge : 419.1407 centred at (gu) : 89.83051 90.35586 91.29050 assigned negative charge : -415.6273 centred at (gu) : 89.59487 90.20828 91.33620 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7793 nv = 96 ne = 84 npr = 56114 no. pairs analyzed = 56114 no. exposed pairs = 3462 no. arc points = 23809 no. surface atoms = 1154 nbur = 1848 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 426 mr = 4380 m= 2 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 31 time to turn everything in is 0.3100000 number of dielectric boundary points 3786 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2324 ## 214 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 9319 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0965271E-08 -8.7382279E-10 midg,1,midg; midg,igrid,midg -1.6192867E-08 3.3016068E-08 1,midg,midg; igrid,midg,midg -3.3692899E-08 4.2805457E-08 gauss-seidel spectral radius is 0.9877467 estimated iterations to convergence 74 setup time was (sec) 0.5300000 now iterating at: 04:25:38 rms-change max change #iterations 0.1624227 23.76605 at 10iterations 1.6743224E-02 2.326974 at 20iterations 1.8746329E-03 0.2506866 at 30iterations 2.6456834E-04 3.6762238E-02 at 40iterations 5.5561188E-05 9.4146729E-03 at 50iterations finished qdiffx linear iterations at : 04:25:40 total time elapsed so far: 2.910000 # loops : 50 mean,max change (kT/e) : 5.5561188E-05 9.4146729E-03 energy calculations done at 2.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.080000 DelPhi exited at 04:25:41 3.082u 0.154s 0:03.73 86.5% 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 04:25:41 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: 331 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3002 !!! WARNING: HIR 43 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.949937 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): -10.46100 37.47400 ymin,ymax (A): -25.90100 22.31500 zmin,zma (A): -8.831000 45.94000 x,y,z range (A): 47.93500 48.21600 54.77100 scale (grids/A): 1.949937 object centre (A): 13.50650 -1.792999 18.55450 number of atom coordinates read : 3002 total number of charged atoms : 2611 net assigned charge : 3.514024 assigned positive charge : 419.1407 centred at (gu) : 89.49093 91.06693 93.87069 assigned negative charge : -415.6273 centred at (gu) : 88.78460 90.62480 94.00826 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 84641 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23809 grid for indexing accessible points = 1.400000 m= 31120 mr = 59659 m= 4825 mr = 23191 m= 303 mr = 2995 m= 4 mr = 139 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 1046 time to turn everything in is 0.5900000 number of dielectric boundary points 34909 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 133 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 20439 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) : 0.6499790 object centre at (A) : 13.50650 -1.792999 18.55450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.5956878E-03 -1.3831146E-02 midg,1,midg; midg,igrid,midg -1.2631343E-02 2.7797667E-02 1,midg,midg; igrid,midg,midg -1.2481396E-02 5.9976272E-02 gauss-seidel spectral radius is 0.9987146 estimated iterations to convergence 221 setup time was (sec) 0.8500000 now iterating at: 04:25:42 rms-change max change #iterations 4.652975 277.3181 at 10iterations 2.235207 72.45276 at 20iterations 1.074308 32.48738 at 30iterations 0.5152863 15.67697 at 40iterations 0.2471856 8.854853 at 50iterations 0.1189268 3.712095 at 60iterations 5.7006571E-02 1.930051 at 70iterations 2.7387228E-02 0.8887177 at 80iterations 1.3154677E-02 0.4013271 at 90iterations 6.2991707E-03 0.1924438 at 100iterations 3.0380068E-03 9.3630493E-02 at 110iterations 1.4722871E-03 4.3254852E-02 at 120iterations finished qdiffx linear iterations at : 04:25:48 total time elapsed so far: 6.840000 # loops : 120 mean,max change (kT/e) : 1.4722871E-03 4.3254852E-02 energy calculations done at 6.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.010000 DelPhi exited at 04:25:48 7.009u 0.173s 0:07.56 94.8% 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 Oct 11 2011 at 04:25:48 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: 331 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3002 !!! WARNING: HIR 43 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.924906 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): -10.46100 37.47400 ymin,ymax (A): -25.90100 22.31500 zmin,zma (A): -8.831000 45.94000 x,y,z range (A): 47.93500 48.21600 54.77100 scale (grids/A): 2.924906 object centre (A): 13.50650 -1.792999 18.55450 number of atom coordinates read : 3002 total number of charged atoms : 2611 net assigned charge : 3.514024 assigned positive charge : 419.1407 centred at (gu) : 89.23631 91.60041 95.80604 assigned negative charge : -415.6273 centred at (gu) : 88.17677 90.93705 96.01247 start vw surface at 0.1600000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 195452 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23809 grid for indexing accessible points = 1.400000 m= 101175 mr = 144072 m= 36597 mr = 83312 m= 8649 mr = 29622 m= 1237 mr = 6411 m= 84 mr = 855 m= 1 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.8600001 no. cavity mid-points inaccessible to solvent = 3481 time to turn everything in is 1.460000 number of dielectric boundary points 78896 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.600000 number of grid points assigned charge 20880 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) : 1.949937 object centre at (A) : 13.50650 -1.792999 18.55450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1054437 5.2663933E-02 midg,1,midg; midg,igrid,midg -0.1402015 0.3379241 1,midg,midg; igrid,midg,midg -7.3864579E-02 0.5200732 gauss-seidel spectral radius is 0.9992759 estimated iterations to convergence 293 setup time was (sec) 1.750000 now iterating at: 04:25:50 rms-change max change #iterations 10.72124 388.0106 at 10iterations 6.299482 203.4400 at 20iterations 3.694035 82.78649 at 30iterations 2.155860 41.46283 at 40iterations 1.257186 24.94062 at 50iterations 0.7325836 13.84510 at 60iterations 0.4258405 8.480428 at 70iterations 0.2477716 4.300233 at 80iterations 0.1441343 2.608929 at 90iterations 8.3652362E-02 1.378954 at 100iterations 4.8591498E-02 0.9324474 at 110iterations 2.8193871E-02 0.5065269 at 120iterations 1.6393863E-02 0.2766275 at 130iterations 9.5656207E-03 0.1808262 at 140iterations 5.5937651E-03 9.1285706E-02 at 150iterations 3.2870048E-03 6.0016632E-02 at 160iterations 1.9609469E-03 3.6195755E-02 at 170iterations 1.1908959E-03 2.3128510E-02 at 180iterations finished qdiffx linear iterations at : 04:26:00 total time elapsed so far: 11.15000 # loops : 180 mean,max change (kT/e) : 1.1908959E-03 2.3128510E-02 energy calculations done at 11.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.33000 DelPhi exited at 04:26:00 11.332u 0.170s 0:12.00 95.8% 0+0k 0+0io 0pf+0w