Tue Oct 11 08:05:39 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 08:05:39 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3396 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5016063 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): 11.19800 73.37100 ymin,ymax (A): -7.549000 63.42300 zmin,zma (A): -10.03200 44.85400 x,y,z range (A): 62.17300 70.97200 54.88600 scale (grids/A): 0.5016063 object centre (A): 42.28450 27.93700 17.41100 number of atom coordinates read : 3396 total number of charged atoms : 3250 net assigned charge : 14.00002 assigned positive charge : 509.4292 centred at (gu) : 89.83693 91.05851 88.95811 assigned negative charge : -495.4307 centred at (gu) : 89.96219 91.14395 88.90649 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 5580 nv = 96 ne = 84 npr = 64150 no. pairs analyzed = 64150 no. exposed pairs = 4842 no. arc points = 34743 no. surface atoms = 1619 nbur = 1777 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.708000 m= 167 mr = 2449 m= 0 mr = 4 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3294 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3359 ## 558 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 7444 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.1685229E-11 1.4896706E-10 midg,1,midg; midg,igrid,midg 1.7859919E-10 3.6164544E-11 1,midg,midg; igrid,midg,midg 2.9566707E-10 -1.9847261E-11 gauss-seidel spectral radius is 0.9795995 estimated iterations to convergence 58 setup time was (sec) 0.6300000 now iterating at: 08:05:40 rms-change max change #iterations 5.1002696E-02 9.501841 at 10iterations 2.5826693E-03 0.4553299 at 20iterations 1.4723433E-04 2.7402878E-02 at 30iterations 1.1141427E-05 1.3980865E-03 at 40iterations 1.3007906E-06 1.2207031E-04 at 50iterations finished qdiffx linear iterations at : 08:05:43 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 1.3007906E-06 1.2207031E-04 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.510000 DelPhi exited at 08:05:44 3.512u 0.177s 0:04.37 84.2% 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 08:05:44 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3396 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: 1.504819 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): 11.19800 73.37100 ymin,ymax (A): -7.549000 63.42300 zmin,zma (A): -10.03200 44.85400 x,y,z range (A): 62.17300 70.97200 54.88600 scale (grids/A): 1.504819 object centre (A): 42.28450 27.93700 17.41100 number of atom coordinates read : 3396 total number of charged atoms : 3250 net assigned charge : 14.00002 assigned positive charge : 509.4292 centred at (gu) : 89.51011 93.17429 86.87362 assigned negative charge : -495.4307 centred at (gu) : 89.88609 93.43130 86.71909 start vw surface at 0.1800000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 61565 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34743 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 15932 mr = 37684 m= 1184 mr = 9798 m= 15 mr = 400 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 154 time to turn everything in is 0.5200000 number of dielectric boundary points 30814 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 530 ## 9 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 24244 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) : 0.5016063 object centre at (A) : 42.28450 27.93700 17.41100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.1920270E-03 4.6242867E-03 midg,1,midg; midg,igrid,midg 1.4695086E-02 -7.8130374E-03 1,midg,midg; igrid,midg,midg 1.5656380E-02 -6.8989181E-04 gauss-seidel spectral radius is 0.9979087 estimated iterations to convergence 174 setup time was (sec) 0.8000000 now iterating at: 08:05:45 rms-change max change #iterations 2.931745 151.0665 at 10iterations 1.145643 49.35664 at 20iterations 0.4441905 18.08672 at 30iterations 0.1728732 6.371342 at 40iterations 6.7684382E-02 2.651876 at 50iterations 2.6310049E-02 0.9899101 at 60iterations 1.0240769E-02 0.3907995 at 70iterations 3.9953939E-03 0.1568117 at 80iterations 1.5599611E-03 6.0332298E-02 at 90iterations 6.0850696E-04 3.0702591E-02 at 100iterations 2.3739698E-04 1.0149002E-02 at 110iterations 9.2786649E-05 3.6811829E-03 at 120iterations finished qdiffx linear iterations at : 08:05:51 total time elapsed so far: 6.930000 # loops : 120 mean,max change (kT/e) : 9.2786649E-05 3.6811829E-03 energy calculations done at 6.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.100000 DelPhi exited at 08:05:51 7.101u 0.169s 0:07.75 93.6% 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 08:05:51 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3396 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.257228 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): 11.19800 73.37100 ymin,ymax (A): -7.549000 63.42300 zmin,zma (A): -10.03200 44.85400 x,y,z range (A): 62.17300 70.97200 54.88600 scale (grids/A): 2.257228 object centre (A): 42.28450 27.93700 17.41100 number of atom coordinates read : 3396 total number of charged atoms : 3250 net assigned charge : 14.00002 assigned positive charge : 509.4292 centred at (gu) : 89.26483 94.76118 85.31011 assigned negative charge : -495.4307 centred at (gu) : 89.82890 95.14666 85.07869 start vw surface at 0.2500000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 143153 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34743 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 57744 mr = 93902 m= 13451 mr = 42601 m= 1528 mr = 9138 m= 69 mr = 834 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.5700000 no. cavity mid-points inaccessible to solvent = 576 time to turn everything in is 1.120000 number of dielectric boundary points 69465 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 73 iepsmp to db, and charging done at 1.250000 number of grid points assigned charge 25911 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) : 1.504819 object centre at (A) : 42.28450 27.93700 17.41100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1535119 6.7723893E-02 midg,1,midg; midg,igrid,midg 0.2310477 -0.1819910 1,midg,midg; igrid,midg,midg 0.2831889 -3.8655259E-02 gauss-seidel spectral radius is 0.9990668 estimated iterations to convergence 259 setup time was (sec) 1.410000 now iterating at: 08:05:53 rms-change max change #iterations 8.190522 250.8454 at 10iterations 4.556134 128.4373 at 20iterations 2.510397 65.39292 at 30iterations 1.368505 33.24549 at 40iterations 0.7435257 19.08020 at 50iterations 0.4028164 9.386092 at 60iterations 0.2175677 4.953508 at 70iterations 0.1173132 3.050880 at 80iterations 6.3212842E-02 1.563898 at 90iterations 3.4019247E-02 0.8269119 at 100iterations 1.8293681E-02 0.4490728 at 110iterations 9.8016784E-03 0.2123051 at 120iterations 5.2592112E-03 0.1131296 at 130iterations 2.8185977E-03 6.1756134E-02 at 140iterations 1.5126875E-03 3.4037471E-02 at 150iterations 8.0923247E-04 1.8463135E-02 at 160iterations 4.3383724E-04 8.8772774E-03 at 170iterations 2.3264490E-04 5.2585602E-03 at 180iterations finished qdiffx linear iterations at : 08:06:03 total time elapsed so far: 10.88000 # loops : 180 mean,max change (kT/e) : 2.3264490E-04 5.2585602E-03 energy calculations done at 10.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.05000 DelPhi exited at 08:06:03 11.054u 0.188s 0:11.77 95.4% 0+0k 0+0io 0pf+0w