Sun Oct 9 11:34:27 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 Sun Oct 9 2011 at 11:34:27 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3122 !!! WARNING: CME 1 has a net charge of -0.0350 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5987923 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): -16.80300 42.30100 ymin,ymax (A): -7.972000 48.22600 zmin,zma (A): -58.59100 0.8620000 x,y,z range (A): 59.10400 56.19800 59.45300 scale (grids/A): 0.5987923 object centre (A): 12.74900 20.12700 -28.86450 number of atom coordinates read : 3122 total number of charged atoms : 3020 net assigned charge : -0.5349858 assigned positive charge : 463.5774 centred at (gu) : 92.00193 91.63659 91.60317 assigned negative charge : -464.1143 centred at (gu) : 91.93389 91.67338 91.54281 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7815 nv = 96 ne = 84 npr = 58810 no. pairs analyzed = 58810 no. exposed pairs = 4561 no. arc points = 33475 no. surface atoms = 1522 nbur = 1600 mkacc time = 0.1200000 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 = 1.456000 m= 379 mr = 3668 m= 5 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 4498 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3276 ## 317 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 9631 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.9583759E-09 3.2000376E-09 midg,1,midg; midg,igrid,midg 8.3960067E-10 -2.6830798E-09 1,midg,midg; igrid,midg,midg -1.9946216E-09 4.0214183E-09 gauss-seidel spectral radius is 0.9856366 estimated iterations to convergence 68 setup time was (sec) 0.5400000 now iterating at: 11:34:28 rms-change max change #iterations 0.1131879 24.03036 at 10iterations 9.6358899E-03 1.405394 at 20iterations 8.1990520E-04 0.1322937 at 30iterations 6.8452995E-05 9.6225739E-03 at 40iterations 6.0874663E-06 1.1482239E-03 at 50iterations finished qdiffx linear iterations at : 11:34:31 total time elapsed so far: 3.370000 # loops : 50 mean,max change (kT/e) : 6.0874663E-06 1.1482239E-03 energy calculations done at 3.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.580000 DelPhi exited at 11:34:31 3.584u 0.137s 0:04.03 92.0% 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 Sun Oct 9 2011 at 11:34:31 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3122 !!! WARNING: CME 1 has a net charge of -0.0350 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: 1.796377 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): -16.80300 42.30100 ymin,ymax (A): -7.972000 48.22600 zmin,zma (A): -58.59100 0.8620000 x,y,z range (A): 59.10400 56.19800 59.45300 scale (grids/A): 1.796377 object centre (A): 12.74900 20.12700 -28.86450 number of atom coordinates read : 3122 total number of charged atoms : 3020 net assigned charge : -0.5349858 assigned positive charge : 463.5774 centred at (gu) : 96.00492 94.90876 94.80849 assigned negative charge : -464.1143 centred at (gu) : 95.80129 95.01988 94.62812 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 84102 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33475 grid for indexing accessible points = 1.400000 m= 27613 mr = 53352 m= 4074 mr = 18592 m= 155 mr = 2237 m= 0 mr = 21 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 703 time to turn everything in is 0.5800000 number of dielectric boundary points 41742 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 234 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 23546 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) : 0.5987923 object centre at (A) : 12.74900 20.12700 -28.86450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.8868696E-02 1.4015701E-02 midg,1,midg; midg,igrid,midg -1.0152341E-02 -5.0034113E-03 1,midg,midg; igrid,midg,midg 2.8949240E-03 7.6869107E-03 gauss-seidel spectral radius is 0.9985554 estimated iterations to convergence 209 setup time was (sec) 0.8300000 now iterating at: 11:34:32 rms-change max change #iterations 4.189267 182.7360 at 10iterations 1.906244 64.19373 at 20iterations 0.8689483 27.49554 at 30iterations 0.3961807 11.98414 at 40iterations 0.1806676 5.926471 at 50iterations 8.2508862E-02 2.631706 at 60iterations 3.7757114E-02 1.224272 at 70iterations 1.7222090E-02 0.5425682 at 80iterations 7.8818118E-03 0.2565765 at 90iterations 3.6032435E-03 0.1259850 at 100iterations 1.6464537E-03 5.5274963E-02 at 110iterations 7.5395603E-04 2.3668289E-02 at 120iterations finished qdiffx linear iterations at : 11:34:38 total time elapsed so far: 6.800000 # loops : 120 mean,max change (kT/e) : 7.5395603E-04 2.3668289E-02 energy calculations done at 6.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.980000 DelPhi exited at 11:34:39 6.980u 0.167s 0:07.44 95.9% 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 Sun Oct 9 2011 at 11:34:39 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3122 !!! WARNING: CME 1 has a net charge of -0.0350 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: 2.694566 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): -16.80300 42.30100 ymin,ymax (A): -7.972000 48.22600 zmin,zma (A): -58.59100 0.8620000 x,y,z range (A): 59.10400 56.19800 59.45300 scale (grids/A): 2.694566 object centre (A): 12.74900 20.12700 -28.86450 number of atom coordinates read : 3122 total number of charged atoms : 3020 net assigned charge : -0.5349858 assigned positive charge : 463.5774 centred at (gu) : 99.00713 97.36286 97.21240 assigned negative charge : -464.1143 centred at (gu) : 98.70197 97.52960 96.94205 start vw surface at 0.1600000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 194520 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33475 grid for indexing accessible points = 1.400000 m= 89761 mr = 131316 m= 31130 mr = 69154 m= 7022 mr = 23411 m= 800 mr = 4854 m= 26 mr = 476 m= 0 mr = 3 time to grow re-entrant surface = 0.8200000 no. cavity mid-points inaccessible to solvent = 2346 time to turn everything in is 1.400000 number of dielectric boundary points 94045 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.530000 number of grid points assigned charge 24151 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) : 1.796377 object centre at (A) : 12.74900 20.12700 -28.86450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4813637 0.1493484 midg,1,midg; midg,igrid,midg -0.1801336 -5.9840791E-02 1,midg,midg; igrid,midg,midg 6.8492159E-02 -4.3891098E-02 gauss-seidel spectral radius is 0.9992651 estimated iterations to convergence 291 setup time was (sec) 1.680000 now iterating at: 11:34:41 rms-change max change #iterations 10.41601 306.8743 at 10iterations 6.236121 165.5948 at 20iterations 3.690654 78.06108 at 30iterations 2.161525 46.45273 at 40iterations 1.267244 24.65781 at 50iterations 0.7371994 14.96204 at 60iterations 0.4281731 9.537430 at 70iterations 0.2478156 4.737349 at 80iterations 0.1436652 2.628052 at 90iterations 8.2903095E-02 1.520615 at 100iterations 4.7978908E-02 0.8893523 at 110iterations 2.7709575E-02 0.5128460 at 120iterations 1.5972909E-02 0.2800436 at 130iterations 9.2048375E-03 0.1641827 at 140iterations 5.3146863E-03 9.2578888E-02 at 150iterations 3.0651218E-03 5.7306051E-02 at 160iterations 1.7646735E-03 3.2600641E-02 at 170iterations 1.0175263E-03 1.7258644E-02 at 180iterations finished qdiffx linear iterations at : 11:34:50 total time elapsed so far: 11.33000 # loops : 180 mean,max change (kT/e) : 1.0175263E-03 1.7258644E-02 energy calculations done at 11.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.50000 DelPhi exited at 11:34:51 11.506u 0.161s 0:11.95 97.5% 0+0k 0+0io 0pf+0w