Tue Nov 22 14:19:17 PST 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 Tue Nov 22 2011 at 14:19:20 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6018292 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): -24.11300 35.04000 ymin,ymax (A): -19.08500 20.47300 zmin,zma (A): -2.485000 38.59300 x,y,z range (A): 59.15300 39.55800 41.07800 scale (grids/A): 0.6018292 object centre (A): 5.463501 0.6940002 18.05400 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 3.000004 assigned positive charge : 287.8241 centred at (gu) : 89.69327 90.32967 90.29710 assigned negative charge : -284.8243 centred at (gu) : 89.69766 90.41927 90.43090 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 4781 nv = 96 ne = 84 npr = 39880 no. pairs analyzed = 39880 no. exposed pairs = 2484 no. arc points = 17109 no. surface atoms = 839 nbur = 1123 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 210 mr = 2606 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.2300000 number of dielectric boundary points 2376 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1769 ## 207 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 5840 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.7904467E-09 -2.6422757E-09 midg,1,midg; midg,igrid,midg 3.6232821E-09 -1.2752499E-09 1,midg,midg; igrid,midg,midg 1.6203989E-09 1.1836003E-09 gauss-seidel spectral radius is 0.9856558 estimated iterations to convergence 68 setup time was (sec) 0.4700000 now iterating at: 14:19:22 rms-change max change #iterations 9.0871386E-02 16.89496 at 10iterations 7.7662067E-03 1.228797 at 20iterations 6.7254651E-04 0.1168447 at 30iterations 5.7988927E-05 1.0284424E-02 at 40iterations 4.9081400E-06 8.1825256E-04 at 50iterations finished qdiffx linear iterations at : 14:19:27 total time elapsed so far: 3.130000 # loops : 50 mean,max change (kT/e) : 4.9081400E-06 8.1825256E-04 energy calculations done at 3.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 14:19:28 3.328u 0.134s 0:08.19 42.1% 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 Nov 22 2011 at 14:19:29 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.805488 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): -24.11300 35.04000 ymin,ymax (A): -19.08500 20.47300 zmin,zma (A): -2.485000 38.59300 x,y,z range (A): 59.15300 39.55800 41.07800 scale (grids/A): 1.805488 object centre (A): 5.463501 0.6940002 18.05400 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 3.000004 assigned positive charge : 287.8241 centred at (gu) : 89.07967 90.98879 90.89114 assigned negative charge : -284.8243 centred at (gu) : 89.09319 91.25786 91.29274 start vw surface at 0.1200000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 51834 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17109 grid for indexing accessible points = 1.400000 m= 18720 mr = 35483 m= 2402 mr = 14092 m= 85 mr = 1414 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 897 time to turn everything in is 0.3900000 number of dielectric boundary points 22043 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 127 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 14266 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) : 0.6018292 object centre at (A) : 5.463501 0.6940002 18.05400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.3087777E-03 -6.2495372E-03 midg,1,midg; midg,igrid,midg 2.4594213E-03 -4.5316233E-03 1,midg,midg; igrid,midg,midg 3.9779946E-02 3.2638580E-02 gauss-seidel spectral radius is 0.9984054 estimated iterations to convergence 199 setup time was (sec) 0.6600000 now iterating at: 14:19:30 rms-change max change #iterations 3.198414 142.4147 at 10iterations 1.404006 61.71716 at 20iterations 0.6201658 22.97999 at 30iterations 0.2714396 11.41871 at 40iterations 0.1203246 4.523590 at 50iterations 5.2683618E-02 1.880112 at 60iterations 2.3220003E-02 0.8929582 at 70iterations 1.0189567E-02 0.3870015 at 80iterations 4.4935970E-03 0.1726780 at 90iterations 1.9715885E-03 8.2200289E-02 at 100iterations 8.7526080E-04 3.5051823E-02 at 110iterations 3.8497074E-04 1.3917208E-02 at 120iterations finished qdiffx linear iterations at : 14:19:44 total time elapsed so far: 7.210000 # loops : 120 mean,max change (kT/e) : 3.8497074E-04 1.3917208E-02 energy calculations done at 7.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.400000 DelPhi exited at 14:19:45 7.401u 0.185s 0:15.75 48.1% 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 Nov 22 2011 at 14:19:45 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.708231 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): -24.11300 35.04000 ymin,ymax (A): -19.08500 20.47300 zmin,zma (A): -2.485000 38.59300 x,y,z range (A): 59.15300 39.55800 41.07800 scale (grids/A): 2.708231 object centre (A): 5.463501 0.6940002 18.05400 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 3.000004 assigned positive charge : 287.8241 centred at (gu) : 88.61955 91.48315 91.33669 assigned negative charge : -284.8243 centred at (gu) : 88.63980 91.88693 91.93915 start vw surface at 0.1100000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 119784 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17109 grid for indexing accessible points = 1.400000 m= 61061 mr = 85867 m= 20944 mr = 50522 m= 4023 mr = 16993 m= 325 mr = 2937 m= 7 mr = 159 m= 0 mr = 0 time to grow re-entrant surface = 0.5700000 no. cavity mid-points inaccessible to solvent = 2991 time to turn everything in is 0.9700000 number of dielectric boundary points 49666 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 14639 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) : 1.805488 object centre at (A) : 5.463501 0.6940002 18.05400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.9056613E-02 -6.3588515E-02 midg,1,midg; midg,igrid,midg 1.2708645E-02 -4.1191570E-02 1,midg,midg; igrid,midg,midg 0.4587678 0.2743508 gauss-seidel spectral radius is 0.9991761 estimated iterations to convergence 275 setup time was (sec) 1.280000 now iterating at: 14:19:52 rms-change max change #iterations 7.741755 252.2379 at 10iterations 4.388947 127.2786 at 20iterations 2.467177 63.59079 at 30iterations 1.381712 38.86640 at 40iterations 0.7726712 19.00278 at 50iterations 0.4311590 8.985142 at 60iterations 0.2397285 5.327021 at 70iterations 0.1338488 3.285965 at 80iterations 7.4557714E-02 1.729446 at 90iterations 4.1439705E-02 0.8510475 at 100iterations 2.3078080E-02 0.5225658 at 110iterations 1.2871538E-02 0.2744904 at 120iterations 7.1367281E-03 0.1617603 at 130iterations 3.9818613E-03 8.5465908E-02 at 140iterations 2.2134092E-03 4.8613548E-02 at 150iterations 1.2291375E-03 3.0574799E-02 at 160iterations 6.8462983E-04 1.5288830E-02 at 170iterations 3.8055168E-04 7.8560114E-03 at 180iterations finished qdiffx linear iterations at : 14:20:27 total time elapsed so far: 11.87000 # loops : 180 mean,max change (kT/e) : 3.8055168E-04 7.8560114E-03 energy calculations done at 11.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.05000 DelPhi exited at 14:20:29 12.056u 0.279s 0:44.31 27.8% 0+0k 0+0io 0pf+0w