Tue Oct 11 03:13:37 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 Tue Oct 11 2011 at 03:13:37 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 = 2670 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: 0.6033694 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): -22.22600 34.90600 ymin,ymax (A): -52.56400 6.438000 zmin,zma (A): -57.93200 0.6140000 x,y,z range (A): 57.13200 59.00200 58.54600 scale (grids/A): 0.6033694 object centre (A): 6.340001 -23.06300 -28.65900 number of atom coordinates read : 2670 total number of charged atoms : 2523 net assigned charge : -2.499990 assigned positive charge : 389.1748 centred at (gu) : 89.17047 88.28990 93.06595 assigned negative charge : -391.6757 centred at (gu) : 89.13032 88.40192 93.18060 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6726 nv = 96 ne = 84 npr = 51330 no. pairs analyzed = 51330 no. exposed pairs = 3885 no. arc points = 27460 no. surface atoms = 1288 nbur = 1382 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 329 mr = 3246 m= 0 mr = 16 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3793 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2671 ## 281 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8225 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7140031E-09 -1.1721080E-08 midg,1,midg; midg,igrid,midg 5.0351128E-09 -3.8391681E-09 1,midg,midg; igrid,midg,midg -3.2621037E-09 4.2314063E-10 gauss-seidel spectral radius is 0.9858051 estimated iterations to convergence 69 setup time was (sec) 0.5100000 now iterating at: 03:13:38 rms-change max change #iterations 0.1123324 16.68373 at 10iterations 9.4984490E-03 1.587066 at 20iterations 8.2111702E-04 0.1238785 at 30iterations 6.9810616E-05 1.0108948E-02 at 40iterations 6.0908487E-06 1.2874603E-03 at 50iterations finished qdiffx linear iterations at : 03:13:41 total time elapsed so far: 2.950000 # loops : 50 mean,max change (kT/e) : 6.0908487E-06 1.2874603E-03 energy calculations done at 2.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.110000 DelPhi exited at 03:13:41 3.117u 0.157s 0:03.63 89.8% 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 03:13:41 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 = 2670 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: 1.810108 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): -22.22600 34.90600 ymin,ymax (A): -52.56400 6.438000 zmin,zma (A): -57.93200 0.6140000 x,y,z range (A): 57.13200 59.00200 58.54600 scale (grids/A): 1.810108 object centre (A): 6.340001 -23.06300 -28.65900 number of atom coordinates read : 2670 total number of charged atoms : 2523 net assigned charge : -2.499990 assigned positive charge : 389.1748 centred at (gu) : 87.51092 84.86923 99.19738 assigned negative charge : -391.6757 centred at (gu) : 87.39114 85.20573 99.54176 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 72790 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27460 grid for indexing accessible points = 1.400000 m= 23517 mr = 46957 m= 2899 mr = 15843 m= 140 mr = 1430 m= 2 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 680 time to turn everything in is 0.5100000 number of dielectric boundary points 35108 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 182 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 19708 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) : 0.6033694 object centre at (A) : 6.340001 -23.06300 -28.65900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3091967E-04 -2.0588947E-02 midg,1,midg; midg,igrid,midg -1.3749129E-02 -2.7996903E-02 1,midg,midg; igrid,midg,midg -8.3769793E-03 2.7939614E-03 gauss-seidel spectral radius is 0.9985104 estimated iterations to convergence 205 setup time was (sec) 0.7600000 now iterating at: 03:13:42 rms-change max change #iterations 3.822540 168.4303 at 10iterations 1.723613 59.65502 at 20iterations 0.7793880 28.12114 at 30iterations 0.3512845 11.89162 at 40iterations 0.1588485 5.244612 at 50iterations 7.1793266E-02 2.566099 at 60iterations 3.2400936E-02 1.108849 at 70iterations 1.4652034E-02 0.5186329 at 80iterations 6.6055208E-03 0.2299347 at 90iterations 2.9875452E-03 0.1033354 at 100iterations 1.3546451E-03 4.6524048E-02 at 110iterations 6.1209721E-04 2.0427704E-02 at 120iterations finished qdiffx linear iterations at : 03:13:48 total time elapsed so far: 6.970000 # loops : 120 mean,max change (kT/e) : 6.1209721E-04 2.0427704E-02 energy calculations done at 6.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.150000 DelPhi exited at 03:13:49 7.155u 0.176s 0:07.64 95.8% 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 03:13:49 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 = 2670 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: 2.715162 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): -22.22600 34.90600 ymin,ymax (A): -52.56400 6.438000 zmin,zma (A): -57.93200 0.6140000 x,y,z range (A): 57.13200 59.00200 58.54600 scale (grids/A): 2.715162 object centre (A): 6.340001 -23.06300 -28.65900 number of atom coordinates read : 2670 total number of charged atoms : 2523 net assigned charge : -2.499990 assigned positive charge : 389.1748 centred at (gu) : 86.26620 82.30360 103.7959 assigned negative charge : -391.6757 centred at (gu) : 86.08666 82.80859 104.3127 start vw surface at 0.1600000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 168463 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27460 grid for indexing accessible points = 1.400000 m= 78501 mr = 115092 m= 24744 mr = 60999 m= 4679 mr = 18326 m= 525 mr = 3043 m= 19 mr = 241 m= 0 mr = 1 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 2316 time to turn everything in is 1.250000 number of dielectric boundary points 79229 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.370000 number of grid points assigned charge 20180 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) : 1.810108 object centre at (A) : 6.340001 -23.06300 -28.65900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.3497801E-02 -0.1301151 midg,1,midg; midg,igrid,midg -1.2133983E-02 -0.4535147 1,midg,midg; igrid,midg,midg -6.3728049E-02 7.8033865E-03 gauss-seidel spectral radius is 0.9992461 estimated iterations to convergence 287 setup time was (sec) 1.520000 now iterating at: 03:13:50 rms-change max change #iterations 9.515100 320.8129 at 10iterations 5.651594 154.0163 at 20iterations 3.303593 78.99678 at 30iterations 1.924987 50.52383 at 40iterations 1.113507 21.76475 at 50iterations 0.6394709 12.32143 at 60iterations 0.3680838 6.990692 at 70iterations 0.2113348 4.525906 at 80iterations 0.1214176 2.401083 at 90iterations 6.9537871E-02 1.337078 at 100iterations 3.9818641E-02 0.7811928 at 110iterations 2.2760207E-02 0.4350190 at 120iterations 1.3007985E-02 0.2501911 at 130iterations 7.4283774E-03 0.1395111 at 140iterations 4.2464803E-03 7.8829288E-02 at 150iterations 2.4227379E-03 4.4496536E-02 at 160iterations 1.3826446E-03 2.5749207E-02 at 170iterations 7.9095556E-04 1.4258265E-02 at 180iterations finished qdiffx linear iterations at : 03:14:00 total time elapsed so far: 10.97000 # loops : 180 mean,max change (kT/e) : 7.9095556E-04 1.4258265E-02 energy calculations done at 10.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.15000 DelPhi exited at 03:14:00 11.155u 0.164s 0:11.62 97.3% 0+0k 0+0io 0pf+0w