Mon Oct 10 14:03:05 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+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 Mon Oct 10 2011 at 14:03:05 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2148 !!! WARNING: LYS 224 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6633623 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): -12.68500 40.98100 ymin,ymax (A): -25.81700 21.96700 zmin,zma (A): -7.487000 36.14000 x,y,z range (A): 53.66600 47.78400 43.62700 scale (grids/A): 0.6633623 object centre (A): 14.14800 -1.925000 14.32650 number of atom coordinates read : 2148 total number of charged atoms : 2006 net assigned charge : -9.271974 assigned positive charge : 322.0198 centred at (gu) : 88.45953 91.14141 89.03555 assigned negative charge : -331.2920 centred at (gu) : 88.74596 91.20111 89.16172 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6423 nv = 96 ne = 84 npr = 44282 no. pairs analyzed = 44282 no. exposed pairs = 2638 no. arc points = 18971 no. surface atoms = 891 nbur = 1257 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 374 mr = 3570 m= 8 mr = 63 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 77 time to turn everything in is 0.1700000 number of dielectric boundary points 3172 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1824 ## 155 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7387 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.2743107E-09 -4.1093195E-08 midg,1,midg; midg,igrid,midg -1.2643156E-08 -4.7515869E-08 1,midg,midg; igrid,midg,midg 3.4458608E-08 -5.8784217E-08 gauss-seidel spectral radius is 0.9881824 estimated iterations to convergence 75 setup time was (sec) 0.3600000 now iterating at: 14:03:05 rms-change max change #iterations 0.1599904 25.08885 at 10iterations 1.7039323E-02 2.945004 at 20iterations 1.8284681E-03 0.2783203 at 30iterations 1.9746713E-04 3.0408859E-02 at 40iterations 2.1255750E-05 3.2017231E-03 at 50iterations finished qdiffx linear iterations at : 14:03:08 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 2.1255750E-05 3.2017231E-03 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 14:03:09 3.356u 0.187s 0:04.26 82.8% 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 Mon Oct 10 2011 at 14:03:09 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2148 !!! WARNING: LYS 224 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.990087 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): -12.68500 40.98100 ymin,ymax (A): -25.81700 21.96700 zmin,zma (A): -7.487000 36.14000 x,y,z range (A): 53.66600 47.78400 43.62700 scale (grids/A): 1.990087 object centre (A): 14.14800 -1.925000 14.32650 number of atom coordinates read : 2148 total number of charged atoms : 2006 net assigned charge : -9.271974 assigned positive charge : 322.0198 centred at (gu) : 85.37827 93.42396 87.10645 assigned negative charge : -331.2920 centred at (gu) : 86.23770 93.60316 87.48522 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 68230 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18971 grid for indexing accessible points = 1.400000 m= 26872 mr = 47048 m= 4985 mr = 20608 m= 346 mr = 3385 m= 4 mr = 144 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 3389 time to turn everything in is 0.3400000 number of dielectric boundary points 29252 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 97 iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 15859 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) : 0.6633623 object centre at (A) : 14.14800 -1.925000 14.32650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.3808014E-03 -3.1958461E-02 midg,1,midg; midg,igrid,midg -3.6404806E-03 -1.5682146E-02 1,midg,midg; igrid,midg,midg 3.4742739E-02 -8.8071905E-02 gauss-seidel spectral radius is 0.9986985 estimated iterations to convergence 220 setup time was (sec) 0.5400000 now iterating at: 14:03:10 rms-change max change #iterations 4.189291 197.0725 at 10iterations 1.995892 82.62970 at 20iterations 0.9485747 37.68489 at 30iterations 0.4512944 16.38663 at 40iterations 0.2158639 7.530359 at 50iterations 0.1027380 3.247307 at 60iterations 4.8762567E-02 1.770353 at 70iterations 2.3295475E-02 0.7590370 at 80iterations 1.1110866E-02 0.3662882 at 90iterations 5.2897600E-03 0.1763906 at 100iterations 2.5150583E-03 8.7262154E-02 at 110iterations 1.2021386E-03 4.1374207E-02 at 120iterations finished qdiffx linear iterations at : 14:03:17 total time elapsed so far: 7.550000 # loops : 120 mean,max change (kT/e) : 1.2021386E-03 4.1374207E-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) 7.680000 DelPhi exited at 14:03:17 7.685u 0.212s 0:08.27 95.4% 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 Mon Oct 10 2011 at 14:03:17 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2148 !!! WARNING: LYS 224 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.985130 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): -12.68500 40.98100 ymin,ymax (A): -25.81700 21.96700 zmin,zma (A): -7.487000 36.14000 x,y,z range (A): 53.66600 47.78400 43.62700 scale (grids/A): 2.985130 object centre (A): 14.14800 -1.925000 14.32650 number of atom coordinates read : 2148 total number of charged atoms : 2006 net assigned charge : -9.271974 assigned positive charge : 322.0198 centred at (gu) : 83.06728 95.13586 85.65958 assigned negative charge : -331.2920 centred at (gu) : 84.35656 95.40485 86.22777 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 157172 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18971 grid for indexing accessible points = 1.400000 m= 83656 mr = 113410 m= 34151 mr = 69639 m= 9330 mr = 28505 m= 1495 mr = 7345 m= 104 mr = 1044 m= 0 mr = 65 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 11906 time to turn everything in is 0.8900000 number of dielectric boundary points 65900 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 16048 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) : 1.990087 object centre at (A) : 14.14800 -1.925000 14.32650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.3310398E-02 -0.2914764 midg,1,midg; midg,igrid,midg -2.3760188E-02 -5.3318672E-02 1,midg,midg; igrid,midg,midg 0.4719832 -0.8331687 gauss-seidel spectral radius is 0.9992648 estimated iterations to convergence 291 setup time was (sec) 1.120000 now iterating at: 14:03:18 rms-change max change #iterations 9.606002 355.7010 at 10iterations 5.561315 130.7522 at 20iterations 3.216881 59.38197 at 30iterations 1.858424 40.69267 at 40iterations 1.070802 20.50100 at 50iterations 0.6175367 14.60176 at 60iterations 0.3553464 6.736397 at 70iterations 0.2045919 4.029460 at 80iterations 0.1177788 2.096846 at 90iterations 6.7734025E-02 1.365955 at 100iterations 3.8922656E-02 0.7280884 at 110iterations 2.2430293E-02 0.4405813 at 120iterations 1.2911770E-02 0.2812157 at 130iterations 7.4016093E-03 0.1375985 at 140iterations 4.2658434E-03 8.6975455E-02 at 150iterations 2.4548473E-03 4.8161656E-02 at 160iterations 1.4114495E-03 2.5817394E-02 at 170iterations 8.1320544E-04 1.6352415E-02 at 180iterations finished qdiffx linear iterations at : 14:03:30 total time elapsed so far: 12.18000 # loops : 180 mean,max change (kT/e) : 8.1320544E-04 1.6352415E-02 energy calculations done at 12.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.32000 DelPhi exited at 14:03:31 12.318u 0.205s 0:13.64 91.7% 0+0k 0+0io 0pf+0w