Mon Oct 10 13:54:36 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 Mon Oct 10 2011 at 13:54:36 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 = 2569 !!! WARNING: GLU 264 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6383704 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): 13.14800 58.68900 ymin,ymax (A): 3.801000 53.44600 zmin,zma (A): -25.98800 29.77900 x,y,z range (A): 45.54100 49.64500 55.76700 scale (grids/A): 0.6383704 object centre (A): 35.91850 28.62350 1.895500 number of atom coordinates read : 2569 total number of charged atoms : 2430 net assigned charge : 1.500004 assigned positive charge : 377.9577 centred at (gu) : 91.45421 90.83675 89.23284 assigned negative charge : -376.4587 centred at (gu) : 91.40857 90.86954 89.42899 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6935 nv = 96 ne = 84 npr = 52146 no. pairs analyzed = 52146 no. exposed pairs = 3494 no. arc points = 24323 no. surface atoms = 1159 nbur = 1410 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 414 mr = 3581 m= 2 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3721 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2362 ## 201 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8413 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6710525E-08 -1.6695862E-08 midg,1,midg; midg,igrid,midg 4.5139772E-09 -2.0434863E-09 1,midg,midg; igrid,midg,midg -2.2195716E-09 9.2840713E-09 gauss-seidel spectral radius is 0.9872893 estimated iterations to convergence 73 setup time was (sec) 0.4000000 now iterating at: 13:54:36 rms-change max change #iterations 0.1388194 22.75413 at 10iterations 1.3659470E-02 1.796474 at 20iterations 1.4583039E-03 0.1932487 at 30iterations 2.7105486E-04 4.0580750E-02 at 40iterations 8.5663160E-05 1.2716293E-02 at 50iterations finished qdiffx linear iterations at : 13:54:39 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 8.5663160E-05 1.2716293E-02 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 13:54:40 3.464u 0.165s 0:04.30 84.1% 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 Mon Oct 10 2011 at 13:54:40 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 = 2569 !!! WARNING: GLU 264 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.915111 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): 13.14800 58.68900 ymin,ymax (A): 3.801000 53.44600 zmin,zma (A): -25.98800 29.77900 x,y,z range (A): 45.54100 49.64500 55.76700 scale (grids/A): 1.915111 object centre (A): 35.91850 28.62350 1.895500 number of atom coordinates read : 2569 total number of charged atoms : 2430 net assigned charge : 1.500004 assigned positive charge : 377.9577 centred at (gu) : 94.36208 92.50967 87.69772 assigned negative charge : -376.4587 centred at (gu) : 94.22541 92.60836 88.28683 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 74585 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24323 grid for indexing accessible points = 1.400000 m= 26946 mr = 49760 m= 4622 mr = 19211 m= 268 mr = 2804 m= 3 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 831 time to turn everything in is 0.3900000 number of dielectric boundary points 34580 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 152 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 19131 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) : 0.6383704 object centre at (A) : 35.91850 28.62350 1.895500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.4911684E-02 -5.7758964E-03 midg,1,midg; midg,igrid,midg 7.6024076E-03 1.2924210E-03 1,midg,midg; igrid,midg,midg -5.6450176E-03 3.4570431E-03 gauss-seidel spectral radius is 0.9986547 estimated iterations to convergence 216 setup time was (sec) 0.6200000 now iterating at: 13:54:41 rms-change max change #iterations 4.245711 179.1060 at 10iterations 1.991840 62.60912 at 20iterations 0.9421037 41.74600 at 30iterations 0.4436385 15.51719 at 40iterations 0.2092336 7.272679 at 50iterations 9.8413788E-02 3.030446 at 60iterations 4.6492048E-02 1.459084 at 70iterations 2.1955123E-02 0.6906033 at 80iterations 1.0420850E-02 0.3156414 at 90iterations 4.9782698E-03 0.1693182 at 100iterations 2.3997526E-03 7.5217247E-02 at 110iterations 1.1862565E-03 4.0813446E-02 at 120iterations finished qdiffx linear iterations at : 13:54:48 total time elapsed so far: 7.800000 # loops : 120 mean,max change (kT/e) : 1.1862565E-03 4.0813446E-02 energy calculations done at 7.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.940000 DelPhi exited at 13:54:49 7.941u 0.204s 0:08.53 95.4% 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 Mon Oct 10 2011 at 13:54:51 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2569 !!! WARNING: GLU 264 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.872667 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): 13.14800 58.68900 ymin,ymax (A): 3.801000 53.44600 zmin,zma (A): -25.98800 29.77900 x,y,z range (A): 45.54100 49.64500 55.76700 scale (grids/A): 2.872667 object centre (A): 35.91850 28.62350 1.895500 number of atom coordinates read : 2569 total number of charged atoms : 2430 net assigned charge : 1.500004 assigned positive charge : 377.9577 centred at (gu) : 96.54282 93.76431 86.54641 assigned negative charge : -376.4587 centred at (gu) : 96.33823 93.91255 87.43018 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 172430 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24323 grid for indexing accessible points = 1.400000 m= 85208 mr = 121404 m= 32280 mr = 67953 m= 8409 mr = 25337 m= 1188 mr = 6194 m= 64 mr = 741 m= 0 mr = 17 time to grow re-entrant surface = 0.5600000 no. cavity mid-points inaccessible to solvent = 3041 time to turn everything in is 0.9800000 number of dielectric boundary points 77933 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 19438 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) : 1.915111 object centre at (A) : 35.91850 28.62350 1.895500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.108131 2.9515896E-02 midg,1,midg; midg,igrid,midg 0.1432525 5.0567668E-02 1,midg,midg; igrid,midg,midg -0.1527010 4.8199981E-02 gauss-seidel spectral radius is 0.9992648 estimated iterations to convergence 291 setup time was (sec) 1.230000 now iterating at: 13:54:53 rms-change max change #iterations 9.924218 336.0298 at 10iterations 5.807431 143.3955 at 20iterations 3.383833 66.44531 at 30iterations 1.966426 36.90837 at 40iterations 1.142023 21.57061 at 50iterations 0.6615570 11.64388 at 60iterations 0.3820803 6.700961 at 70iterations 0.2207836 4.119903 at 80iterations 0.1274241 2.435246 at 90iterations 7.3613115E-02 1.372986 at 100iterations 4.2365156E-02 0.7897644 at 110iterations 2.4429087E-02 0.4670178 at 120iterations 1.4076634E-02 0.2706757 at 130iterations 8.1159323E-03 0.1485100 at 140iterations 4.6888716E-03 9.8133087E-02 at 150iterations 2.7018010E-03 5.1940441E-02 at 160iterations 1.5686415E-03 2.7212143E-02 at 170iterations 9.1491133E-04 1.7616272E-02 at 180iterations finished qdiffx linear iterations at : 13:55:05 total time elapsed so far: 12.91000 # loops : 180 mean,max change (kT/e) : 9.1491133E-04 1.7616272E-02 energy calculations done at 12.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.04000 DelPhi exited at 13:55:05 13.047u 0.223s 0:13.65 97.1% 0+0k 0+0io 0pf+0w