Sun Oct 9 23:17:47 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 23:17:47 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2259 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: 0.6695631 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): -12.14100 33.15300 ymin,ymax (A): -22.17700 28.11500 zmin,zma (A): -10.60500 42.56400 x,y,z range (A): 45.29400 50.29200 53.16900 scale (grids/A): 0.6695631 object centre (A): 10.50600 2.969000 15.97950 number of atom coordinates read : 2259 total number of charged atoms : 2120 net assigned charge : 2.500005 assigned positive charge : 335.5795 centred at (gu) : 91.46248 91.26368 90.50533 assigned negative charge : -333.0798 centred at (gu) : 91.43159 91.12711 90.24311 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7064 nv = 96 ne = 84 npr = 44128 no. pairs analyzed = 44128 no. exposed pairs = 2928 no. arc points = 20639 no. surface atoms = 993 nbur = 1266 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 376 mr = 3855 m= 3 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.2700000 number of dielectric boundary points 3537 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1848 ## 181 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7948 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.5527567E-08 6.9342335E-08 midg,1,midg; midg,igrid,midg -1.7141902E-08 4.7426187E-08 1,midg,midg; igrid,midg,midg 6.5883959E-10 1.8967592E-08 gauss-seidel spectral radius is 0.9884137 estimated iterations to convergence 76 setup time was (sec) 0.5200000 now iterating at: 23:17:48 rms-change max change #iterations 0.1631525 25.18168 at 10iterations 1.8002369E-02 2.823936 at 20iterations 1.9797292E-03 0.2739258 at 30iterations 2.4023229E-04 3.5778046E-02 at 40iterations 5.2625568E-05 9.3274117E-03 at 50iterations finished qdiffx linear iterations at : 23:17:51 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 5.2625568E-05 9.3274117E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 23:17:51 3.385u 0.213s 0:03.85 93.2% 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 Sun Oct 9 2011 at 23:17:51 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2259 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.008689 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): -12.14100 33.15300 ymin,ymax (A): -22.17700 28.11500 zmin,zma (A): -10.60500 42.56400 x,y,z range (A): 45.29400 50.29200 53.16900 scale (grids/A): 2.008689 object centre (A): 10.50600 2.969000 15.97950 number of atom coordinates read : 2259 total number of charged atoms : 2120 net assigned charge : 2.500005 assigned positive charge : 335.5795 centred at (gu) : 94.38728 93.79082 91.51579 assigned negative charge : -333.0798 centred at (gu) : 94.29475 93.38120 90.72913 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 75923 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20639 grid for indexing accessible points = 1.400000 m= 27752 mr = 52231 m= 4660 mr = 20500 m= 353 mr = 3018 m= 5 mr = 183 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 1269 time to turn everything in is 0.5400000 number of dielectric boundary points 32761 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 101 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 16787 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) : 0.6695631 object centre at (A) : 10.50600 2.969000 15.97950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.9671877E-02 5.5876328E-03 midg,1,midg; midg,igrid,midg 1.9099072E-02 7.2698094E-02 1,midg,midg; igrid,midg,midg -1.5640136E-02 -1.0893515E-03 gauss-seidel spectral radius is 0.9987417 estimated iterations to convergence 223 setup time was (sec) 0.8400000 now iterating at: 23:17:52 rms-change max change #iterations 4.354043 185.2405 at 10iterations 2.095001 76.66951 at 20iterations 1.009381 33.60648 at 30iterations 0.4882668 15.37615 at 40iterations 0.2368567 6.809275 at 50iterations 0.1145948 3.173876 at 60iterations 5.5411033E-02 1.806881 at 70iterations 2.6709378E-02 0.8920860 at 80iterations 1.2974246E-02 0.4166965 at 90iterations 6.3411850E-03 0.1943645 at 100iterations 3.1363829E-03 0.1206379 at 110iterations 1.6002906E-03 5.1941872E-02 at 120iterations finished qdiffx linear iterations at : 23:17:59 total time elapsed so far: 7.470000 # loops : 120 mean,max change (kT/e) : 1.6002906E-03 5.1941872E-02 energy calculations done at 7.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.640000 DelPhi exited at 23:18:00 7.638u 0.247s 0:08.28 95.0% 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 23:18:00 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2259 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: 3.013034 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): -12.14100 33.15300 ymin,ymax (A): -22.17700 28.11500 zmin,zma (A): -10.60500 42.56400 x,y,z range (A): 45.29400 50.29200 53.16900 scale (grids/A): 3.013034 object centre (A): 10.50600 2.969000 15.97950 number of atom coordinates read : 2259 total number of charged atoms : 2120 net assigned charge : 2.500005 assigned positive charge : 335.5795 centred at (gu) : 96.58084 95.68600 92.27349 assigned negative charge : -333.0798 centred at (gu) : 96.44204 95.07169 91.09357 start vw surface at 0.1500000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 175331 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20639 grid for indexing accessible points = 1.400000 m= 89332 mr = 126302 m= 32751 mr = 73079 m= 8456 mr = 26454 m= 1562 mr = 6560 m= 158 mr = 1147 m= 5 mr = 112 m= 0 mr = 0 time to grow re-entrant surface = 0.8000000 no. cavity mid-points inaccessible to solvent = 3899 time to turn everything in is 1.400000 number of dielectric boundary points 73941 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.540000 number of grid points assigned charge 16960 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) : 2.008689 object centre at (A) : 10.50600 2.969000 15.97950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5986823 -0.1127047 midg,1,midg; midg,igrid,midg 0.2234354 0.7486584 1,midg,midg; igrid,midg,midg -0.2087892 -9.3097486E-05 gauss-seidel spectral radius is 0.9992883 estimated iterations to convergence 296 setup time was (sec) 1.720000 now iterating at: 23:18:02 rms-change max change #iterations 10.06947 330.6691 at 10iterations 5.940262 147.8753 at 20iterations 3.497831 77.28204 at 30iterations 2.056523 41.80381 at 40iterations 1.207199 23.94684 at 50iterations 0.7056795 13.11554 at 60iterations 0.4114571 7.800282 at 70iterations 0.2402506 4.583076 at 80iterations 0.1401435 2.592167 at 90iterations 8.1557341E-02 1.481584 at 100iterations 4.7522482E-02 0.8531616 at 110iterations 2.7660104E-02 0.4963415 at 120iterations 1.6104180E-02 0.3003139 at 130iterations 9.3810940E-03 0.1563950 at 140iterations 5.4572709E-03 9.7923279E-02 at 150iterations 3.1718677E-03 5.7579041E-02 at 160iterations 1.8429453E-03 3.1208038E-02 at 170iterations 1.0725632E-03 1.8283844E-02 at 180iterations finished qdiffx linear iterations at : 23:18:12 total time elapsed so far: 12.46000 # loops : 180 mean,max change (kT/e) : 1.0725632E-03 1.8283844E-02 energy calculations done at 12.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.63000 DelPhi exited at 23:18:13 12.633u 0.262s 0:13.22 97.5% 0+0k 0+0io 0pf+0w