Sun Oct 9 23:46:05 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+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 Sun Oct 9 2011 at 23:46:05 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3141 !!! WARNING: SEP 138 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5909695 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): -30.12600 30.11400 ymin,ymax (A): 7.942000 61.88600 zmin,zma (A): 25.04600 76.19600 x,y,z range (A): 60.24000 53.94400 51.15000 scale (grids/A): 0.5909695 object centre (A): -5.9995651E-03 34.91400 50.62100 number of atom coordinates read : 3141 total number of charged atoms : 2994 net assigned charge : 2.5008768E-02 assigned positive charge : 474.4530 centred at (gu) : 89.99977 89.02129 89.24686 assigned negative charge : -474.4292 centred at (gu) : 90.02016 89.03924 89.36231 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7296 nv = 96 ne = 84 npr = 62765 no. pairs analyzed = 62765 no. exposed pairs = 4114 no. arc points = 29023 no. surface atoms = 1374 nbur = 1767 mkacc time = 9.9999994E-02 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= 309 mr = 3813 m= 0 mr = 8 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3784 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2897 ## 315 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 9181 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.5278030E-09 -3.3173810E-09 midg,1,midg; midg,igrid,midg 7.1984146E-10 -5.0338655E-10 1,midg,midg; igrid,midg,midg 6.5309064E-10 -7.1468892E-10 gauss-seidel spectral radius is 0.9852347 estimated iterations to convergence 68 setup time was (sec) 0.4100000 now iterating at: 23:46:06 rms-change max change #iterations 0.1113921 19.02182 at 10iterations 9.1834767E-03 1.494225 at 20iterations 7.4294076E-04 9.9466085E-02 at 30iterations 6.2338193E-05 9.2620850E-03 at 40iterations 5.1666789E-06 8.8906288E-04 at 50iterations finished qdiffx linear iterations at : 23:46:09 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 5.1666789E-06 8.8906288E-04 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 23:46:09 3.435u 0.184s 0:03.88 93.0% 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 23:46:09 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3141 !!! WARNING: SEP 138 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.772908 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): -30.12600 30.11400 ymin,ymax (A): 7.942000 61.88600 zmin,zma (A): 25.04600 76.19600 x,y,z range (A): 60.24000 53.94400 51.15000 scale (grids/A): 1.772908 object centre (A): -5.9995651E-03 34.91400 50.62100 number of atom coordinates read : 3141 total number of charged atoms : 2994 net assigned charge : 2.5008768E-02 assigned positive charge : 474.4530 centred at (gu) : 89.99821 87.06291 87.73970 assigned negative charge : -474.4292 centred at (gu) : 90.06003 87.11757 88.08655 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 79751 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29023 grid for indexing accessible points = 1.400000 m= 25245 mr = 53871 m= 3019 mr = 17556 m= 103 mr = 1605 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 1549 time to turn everything in is 0.3800000 number of dielectric boundary points 35071 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 284 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 23354 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) : 0.5909695 object centre at (A) : -5.9995651E-03 34.91400 50.62100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.3917996E-03 -3.6398426E-03 midg,1,midg; midg,igrid,midg 7.4163866E-03 7.3398273E-03 1,midg,midg; igrid,midg,midg 1.2263772E-02 -7.4523017E-03 gauss-seidel spectral radius is 0.9984955 estimated iterations to convergence 204 setup time was (sec) 0.5900000 now iterating at: 23:46:10 rms-change max change #iterations 4.122460 188.8361 at 10iterations 1.848371 62.87206 at 20iterations 0.8299873 28.53594 at 30iterations 0.3752679 13.29257 at 40iterations 0.1685614 5.383896 at 50iterations 7.6014608E-02 2.797112 at 60iterations 3.4264758E-02 1.149517 at 70iterations 1.5402975E-02 0.5265656 at 80iterations 6.9173258E-03 0.2162094 at 90iterations 3.1322436E-03 0.1062067 at 100iterations 1.4148644E-03 4.5453310E-02 at 110iterations 6.3771225E-04 1.9645691E-02 at 120iterations finished qdiffx linear iterations at : 23:46:17 total time elapsed so far: 7.730000 # loops : 120 mean,max change (kT/e) : 6.3771225E-04 1.9645691E-02 energy calculations done at 7.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.870000 DelPhi exited at 23:46:18 7.870u 0.211s 0:08.44 95.7% 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 23:46:18 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3141 !!! WARNING: SEP 138 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.659363 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): -30.12600 30.11400 ymin,ymax (A): 7.942000 61.88600 zmin,zma (A): 25.04600 76.19600 x,y,z range (A): 60.24000 53.94400 51.15000 scale (grids/A): 2.659363 object centre (A): -5.9995651E-03 34.91400 50.62100 number of atom coordinates read : 3141 total number of charged atoms : 2994 net assigned charge : 2.5008768E-02 assigned positive charge : 474.4530 centred at (gu) : 89.99723 85.59418 86.60934 assigned negative charge : -474.4292 centred at (gu) : 90.08997 85.67625 87.12979 start vw surface at 0.1000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 185116 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29023 grid for indexing accessible points = 1.400000 m= 85828 mr = 131896 m= 26119 mr = 68063 m= 4810 mr = 19813 m= 436 mr = 3340 m= 8 mr = 203 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 5480 time to turn everything in is 0.9600000 number of dielectric boundary points 79002 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.060000 number of grid points assigned charge 23944 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) : 1.772908 object centre at (A) : -5.9995651E-03 34.91400 50.62100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1321691 6.3025504E-03 midg,1,midg; midg,igrid,midg 7.1033850E-02 0.1082984 1,midg,midg; igrid,midg,midg 0.1169544 -8.1355162E-02 gauss-seidel spectral radius is 0.9992437 estimated iterations to convergence 287 setup time was (sec) 1.200000 now iterating at: 23:46:19 rms-change max change #iterations 10.23324 346.0809 at 10iterations 6.021137 152.9878 at 20iterations 3.514124 77.23288 at 30iterations 2.040360 43.39304 at 40iterations 1.180215 22.91927 at 50iterations 0.6817961 14.73793 at 60iterations 0.3936527 7.164017 at 70iterations 0.2259081 4.506012 at 80iterations 0.1297631 2.591406 at 90iterations 7.4530371E-02 1.370544 at 100iterations 4.2690817E-02 0.9296565 at 110iterations 2.4387566E-02 0.5072408 at 120iterations 1.3971101E-02 0.2993774 at 130iterations 7.9895798E-03 0.1610837 at 140iterations 4.5766151E-03 8.9075089E-02 at 150iterations 2.6120730E-03 4.5837402E-02 at 160iterations 1.4947639E-03 2.7267456E-02 at 170iterations 8.5348415E-04 1.5276909E-02 at 180iterations finished qdiffx linear iterations at : 23:46:30 total time elapsed so far: 12.62000 # loops : 180 mean,max change (kT/e) : 8.5348415E-04 1.5276909E-02 energy calculations done at 12.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.74000 DelPhi exited at 23:46:31 12.747u 0.215s 0:13.25 97.7% 0+0k 0+0io 0pf+0w