Sun Oct 9 16:56:11 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 16:56:12 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5011 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.5460709 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): -46.97800 18.21500 ymin,ymax (A): -37.78300 25.14100 zmin,zma (A): 10.89400 72.61800 x,y,z range (A): 65.19300 62.92400 61.72400 scale (grids/A): 0.5460709 object centre (A): -14.38150 -6.320999 41.75600 number of atom coordinates read : 5011 total number of charged atoms : 4901 net assigned charge : 5.000073 assigned positive charge : 764.6407 centred at (gu) : 89.67679 89.63536 89.33821 assigned negative charge : -759.6456 centred at (gu) : 89.69214 89.49653 89.24807 start vw surface at 0.2400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 9676 nv = 96 ne = 84 npr = 99849 no. pairs analyzed = 99849 no. exposed pairs = 6290 no. arc points = 43538 no. surface atoms = 2092 nbur = 2919 mkacc time = 0.2300000 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 = 1.568000 m= 424 mr = 5190 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.5400000 number of dielectric boundary points 4897 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4536 ## 612 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 13005 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.4381946E-10 1.1394393E-09 midg,1,midg; midg,igrid,midg -1.4073429E-09 1.7181809E-09 1,midg,midg; igrid,midg,midg 5.4324606E-10 1.4137841E-10 gauss-seidel spectral radius is 0.9828671 estimated iterations to convergence 63 setup time was (sec) 0.7800000 now iterating at: 16:56:12 rms-change max change #iterations 0.1018530 13.75435 at 10iterations 8.8008763E-03 1.239487 at 20iterations 1.4790314E-03 0.1739502 at 30iterations 4.0702202E-04 4.5982361E-02 at 40iterations 1.2643503E-04 1.4022827E-02 at 50iterations finished qdiffx linear iterations at : 16:56:15 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 1.2643503E-04 1.4022827E-02 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.600000 DelPhi exited at 16:56:16 3.606u 0.156s 0:04.15 90.3% 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 16:56:16 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5011 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.638213 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): -46.97800 18.21500 ymin,ymax (A): -37.78300 25.14100 zmin,zma (A): 10.89400 72.61800 x,y,z range (A): 65.19300 62.92400 61.72400 scale (grids/A): 1.638213 object centre (A): -14.38150 -6.320999 41.75600 number of atom coordinates read : 5011 total number of charged atoms : 4901 net assigned charge : 5.000073 assigned positive charge : 764.6407 centred at (gu) : 89.02888 88.90495 88.01324 assigned negative charge : -759.6456 centred at (gu) : 89.07607 88.48924 87.74371 start vw surface at 0.2100000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 108486 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43538 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 33454 mr = 75326 m= 3494 mr = 22982 m= 142 mr = 1729 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 1045 time to turn everything in is 0.7500000 number of dielectric boundary points 45531 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 509 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 37595 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) : 0.5460709 object centre at (A) : -14.38150 -6.320999 41.75600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4506251E-02 4.1302629E-02 midg,1,midg; midg,igrid,midg -2.5733434E-02 3.0308614E-02 1,midg,midg; igrid,midg,midg 1.0859045E-02 -3.8249407E-02 gauss-seidel spectral radius is 0.9984133 estimated iterations to convergence 199 setup time was (sec) 1.040000 now iterating at: 16:56:17 rms-change max change #iterations 4.604140 158.3190 at 10iterations 2.023920 69.91272 at 20iterations 0.8916759 27.50808 at 30iterations 0.3943965 10.93880 at 40iterations 0.1746309 5.638687 at 50iterations 7.7401929E-02 2.109381 at 60iterations 3.4246568E-02 0.9751358 at 70iterations 1.5233463E-02 0.4320526 at 80iterations 6.8407292E-03 0.1902885 at 90iterations 3.1200992E-03 9.9151611E-02 at 100iterations 1.4646646E-03 4.2564392E-02 at 110iterations 7.2363409E-04 1.9577026E-02 at 120iterations finished qdiffx linear iterations at : 16:56:24 total time elapsed so far: 7.670000 # loops : 120 mean,max change (kT/e) : 7.2363409E-04 1.9577026E-02 energy calculations done at 7.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.860000 DelPhi exited at 16:56:24 7.862u 0.180s 0:08.41 95.6% 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 16:56:24 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5011 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.457319 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): -46.97800 18.21500 ymin,ymax (A): -37.78300 25.14100 zmin,zma (A): 10.89400 72.61800 x,y,z range (A): 65.19300 62.92400 61.72400 scale (grids/A): 2.457319 object centre (A): -14.38150 -6.320999 41.75600 number of atom coordinates read : 5011 total number of charged atoms : 4901 net assigned charge : 5.000073 assigned positive charge : 764.6407 centred at (gu) : 88.54301 88.35677 87.01948 assigned negative charge : -759.6456 centred at (gu) : 88.61395 87.73365 86.61539 start vw surface at 0.2100000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 252651 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43538 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 116421 mr = 184709 m= 33125 mr = 92093 m= 5362 mr = 24833 m= 378 mr = 3568 m= 7 mr = 149 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 1.110000 no. cavity mid-points inaccessible to solvent = 3693 time to turn everything in is 1.840000 number of dielectric boundary points 102593 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 33 iepsmp to db, and charging done at 1.990000 number of grid points assigned charge 39170 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) : 1.638213 object centre at (A) : -14.38150 -6.320999 41.75600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3591128 0.6487821 midg,1,midg; midg,igrid,midg -0.5342925 0.3855219 1,midg,midg; igrid,midg,midg 0.1574529 -0.9983318 gauss-seidel spectral radius is 0.9992599 estimated iterations to convergence 290 setup time was (sec) 2.160000 now iterating at: 16:56:27 rms-change max change #iterations 11.97907 301.0499 at 10iterations 7.145989 149.1052 at 20iterations 4.231468 91.92582 at 30iterations 2.491524 54.40074 at 40iterations 1.461551 30.47643 at 50iterations 0.8521877 15.80347 at 60iterations 0.4971152 9.638081 at 70iterations 0.2890683 5.478970 at 80iterations 0.1671872 3.036753 at 90iterations 9.6973389E-02 1.673773 at 100iterations 5.6011345E-02 0.9603087 at 110iterations 3.2388091E-02 0.5553002 at 120iterations 1.8710857E-02 0.3191024 at 130iterations 1.0803787E-02 0.1807775 at 140iterations 6.2548351E-03 0.1116562 at 150iterations 3.6123411E-03 6.1972618E-02 at 160iterations 2.0977189E-03 3.4874856E-02 at 170iterations 1.2230674E-03 2.1739960E-02 at 180iterations finished qdiffx linear iterations at : 16:56:37 total time elapsed so far: 12.85000 # loops : 180 mean,max change (kT/e) : 1.2230674E-03 2.1739960E-02 energy calculations done at 12.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.03000 DelPhi exited at 16:56:38 13.031u 0.210s 0:13.54 97.7% 0+0k 0+0io 0pf+0w