Tue Oct 11 03:40:03 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 03:40:04 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2869 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 0.6706478 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): -9.342999 36.59300 ymin,ymax (A): -26.78100 21.27800 zmin,zma (A): -7.845000 45.23800 x,y,z range (A): 45.93600 48.05900 53.08300 scale (grids/A): 0.6706478 object centre (A): 13.62500 -2.751500 18.69650 number of atom coordinates read : 2869 total number of charged atoms : 2703 net assigned charge : 1.162021 assigned positive charge : 430.0116 centred at (gu) : 89.54141 90.69970 91.24169 assigned negative charge : -428.8503 centred at (gu) : 89.21170 90.60084 91.26006 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8498 nv = 96 ne = 84 npr = 59848 no. pairs analyzed = 59848 no. exposed pairs = 3271 no. arc points = 22689 no. surface atoms = 1115 nbur = 1754 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 521 mr = 5015 m= 5 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 64 time to turn everything in is 0.3400000 number of dielectric boundary points 3940 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2210 ## 199 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 10100 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.5133455E-09 -1.1282247E-09 midg,1,midg; midg,igrid,midg -2.0763954E-08 3.7444490E-08 1,midg,midg; igrid,midg,midg -1.0239859E-07 8.6664912E-08 gauss-seidel spectral radius is 0.9884908 estimated iterations to convergence 76 setup time was (sec) 0.6000000 now iterating at: 03:40:04 rms-change max change #iterations 0.1947263 28.27068 at 10iterations 2.2001067E-02 2.960787 at 20iterations 2.4840517E-03 0.3734627 at 30iterations 3.0137014E-04 3.8112640E-02 at 40iterations 5.1280978E-05 6.2103271E-03 at 50iterations finished qdiffx linear iterations at : 03:40:08 total time elapsed so far: 4.390000 # loops : 50 mean,max change (kT/e) : 5.1280978E-05 6.2103271E-03 energy calculations done at 4.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.570000 DelPhi exited at 03:40:09 4.570u 0.390s 0:05.32 93.2% 0+0k 0+0io 6pf+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 03:40:09 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2869 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 2.011943 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): -9.342999 36.59300 ymin,ymax (A): -26.78100 21.27800 zmin,zma (A): -7.845000 45.23800 x,y,z range (A): 45.93600 48.05900 53.08300 scale (grids/A): 2.011943 object centre (A): 13.62500 -2.751500 18.69650 number of atom coordinates read : 2869 total number of charged atoms : 2703 net assigned charge : 1.162021 assigned positive charge : 430.0116 centred at (gu) : 88.62374 92.09885 93.72462 assigned negative charge : -428.8503 centred at (gu) : 87.63480 91.80226 93.77975 start vw surface at 0.1200000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 90850 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22689 grid for indexing accessible points = 1.400000 m= 36660 mr = 65439 m= 6510 mr = 28296 m= 454 mr = 4296 m= 11 mr = 190 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 3067 time to turn everything in is 0.7400000 number of dielectric boundary points 36264 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 121 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 21406 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) : 0.6706478 object centre at (A) : 13.62500 -2.751500 18.69650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.5200894E-03 1.0657745E-02 midg,1,midg; midg,igrid,midg -1.3181163E-02 9.7114965E-03 1,midg,midg; igrid,midg,midg -3.5654541E-02 7.1469150E-02 gauss-seidel spectral radius is 0.9987877 estimated iterations to convergence 227 setup time was (sec) 1.110000 now iterating at: 03:40:10 rms-change max change #iterations 4.959821 200.1207 at 10iterations 2.441634 90.22736 at 20iterations 1.198051 34.79706 at 30iterations 0.5885465 16.93265 at 40iterations 0.2890820 8.330750 at 50iterations 0.1416878 4.268471 at 60iterations 6.9583982E-02 2.019313 at 70iterations 3.4186173E-02 0.9298477 at 80iterations 1.6761543E-02 0.4693842 at 90iterations 8.1959330E-03 0.2296600 at 100iterations 4.0271017E-03 0.1049538 at 110iterations 1.9838933E-03 6.2269211E-02 at 120iterations finished qdiffx linear iterations at : 03:40:21 total time elapsed so far: 11.85000 # loops : 120 mean,max change (kT/e) : 1.9838933E-03 6.2269211E-02 energy calculations done at 11.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.02000 DelPhi exited at 03:40:22 12.029u 0.445s 0:12.85 96.9% 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 03:40:22 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2869 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 3.017915 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): -9.342999 36.59300 ymin,ymax (A): -26.78100 21.27800 zmin,zma (A): -7.845000 45.23800 x,y,z range (A): 45.93600 48.05900 53.08300 scale (grids/A): 3.017915 object centre (A): 13.62500 -2.751500 18.69650 number of atom coordinates read : 2869 total number of charged atoms : 2703 net assigned charge : 1.162021 assigned positive charge : 430.0116 centred at (gu) : 87.93557 93.14794 95.58690 assigned negative charge : -428.8503 centred at (gu) : 86.45207 92.70336 95.66963 start vw surface at 0.1200000 fill in re-entrant regions at 0.6300000 boundary points on vw surface= 209536 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22689 grid for indexing accessible points = 1.400000 m= 114314 mr = 157132 m= 46330 mr = 95988 m= 12127 mr = 38743 m= 1880 mr = 9367 m= 162 mr = 1300 m= 3 mr = 82 m= 0 mr = 2 time to grow re-entrant surface = 1.240000 no. cavity mid-points inaccessible to solvent = 9931 time to turn everything in is 2.000000 number of dielectric boundary points 81738 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.130000 number of grid points assigned charge 21623 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) : 2.011943 object centre at (A) : 13.62500 -2.751500 18.69650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4768632E-03 0.3538140 midg,1,midg; midg,igrid,midg -0.1536105 5.2941076E-02 1,midg,midg; igrid,midg,midg -0.1863978 0.5929621 gauss-seidel spectral radius is 0.9992952 estimated iterations to convergence 297 setup time was (sec) 2.340000 now iterating at: 03:40:24 rms-change max change #iterations 11.34214 425.3759 at 10iterations 6.717437 136.4983 at 20iterations 3.972698 74.88921 at 30iterations 2.340574 42.49702 at 40iterations 1.377591 23.39516 at 50iterations 0.8091962 14.40116 at 60iterations 0.4751002 7.902653 at 70iterations 0.2781424 4.449234 at 80iterations 0.1628891 2.534363 at 90iterations 9.5232286E-02 1.576893 at 100iterations 5.5769056E-02 0.8938293 at 110iterations 3.2563951E-02 0.5242996 at 120iterations 1.9089451E-02 0.3522162 at 130iterations 1.1191216E-02 0.1932278 at 140iterations 6.5519665E-03 0.1074238 at 150iterations 3.8498812E-03 6.5044403E-02 at 160iterations 2.2809580E-03 3.9798737E-02 at 170iterations 1.3699074E-03 2.4715424E-02 at 180iterations finished qdiffx linear iterations at : 03:40:41 total time elapsed so far: 18.90000 # loops : 180 mean,max change (kT/e) : 1.3699074E-03 2.4715424E-02 energy calculations done at 18.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.07000 DelPhi exited at 03:40:42 19.075u 0.469s 0:20.05 97.4% 0+0k 0+0io 0pf+0w