Sat Oct 15 13:59:48 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 Sat Oct 15 2011 at 13:59:49 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: 334 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4449 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: ZN8 820 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 0.5116486 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): -17.21500 37.42800 ymin,ymax (A): -33.09100 32.45000 zmin,zma (A): -4.023000 65.55600 x,y,z range (A): 54.64300 65.54100 69.57900 scale (grids/A): 0.5116486 object centre (A): 10.10650 -0.3204994 30.76650 number of atom coordinates read : 4449 total number of charged atoms : 4201 net assigned charge : 3.606023 assigned positive charge : 662.1941 centred at (gu) : 90.34987 90.95769 87.54658 assigned negative charge : -658.5922 centred at (gu) : 90.20882 90.99174 87.56469 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7443 nv = 96 ne = 84 npr = 90149 no. pairs analyzed = 90149 no. exposed pairs = 5701 no. arc points = 39498 no. surface atoms = 1894 nbur = 2555 mkacc time = 0.1500000 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 = 1.680000 m= 269 mr = 3822 m= 0 mr = 11 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3879 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3799 ## 554 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 9857 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8460862E-10 4.2868387E-12 midg,1,midg; midg,igrid,midg 1.0567641E-10 -4.3611992E-11 1,midg,midg; igrid,midg,midg -2.7725550E-10 4.3325482E-10 gauss-seidel spectral radius is 0.9804435 estimated iterations to convergence 59 setup time was (sec) 0.5300000 now iterating at: 13:59:50 rms-change max change #iterations 6.7085110E-02 9.802929 at 10iterations 3.9712205E-03 0.5947437 at 20iterations 4.4837457E-04 6.7230225E-02 at 30iterations 1.5051136E-04 2.3672581E-02 at 40iterations 5.8267444E-05 9.1228485E-03 at 50iterations finished qdiffx linear iterations at : 13:59:55 total time elapsed so far: 3.520000 # loops : 50 mean,max change (kT/e) : 5.8267444E-05 9.1228485E-03 energy calculations done at 3.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.650000 DelPhi exited at 13:59:57 3.653u 0.212s 0:08.43 45.7% 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 Sat Oct 15 2011 at 13:59:58 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: 334 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4449 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: ZN8 820 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 1.534946 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): -17.21500 37.42800 ymin,ymax (A): -33.09100 32.45000 zmin,zma (A): -4.023000 65.55600 x,y,z range (A): 54.64300 65.54100 69.57900 scale (grids/A): 1.534946 object centre (A): 10.10650 -0.3204994 30.76650 number of atom coordinates read : 4449 total number of charged atoms : 4201 net assigned charge : 3.606023 assigned positive charge : 662.1941 centred at (gu) : 91.04855 92.87155 82.63869 assigned negative charge : -658.5922 centred at (gu) : 90.62620 92.97501 82.69377 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 84308 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39498 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 23989 mr = 57795 m= 2127 mr = 15800 m= 49 mr = 881 m= 0 mr = 4 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 55 time to turn everything in is 0.4100000 number of dielectric boundary points 35993 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 502 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 31628 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) : 0.5116486 object centre at (A) : 10.10650 -0.3204994 30.76650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4251608E-03 8.0124130E-03 midg,1,midg; midg,igrid,midg -1.7991959E-03 -1.1609369E-02 1,midg,midg; igrid,midg,midg -4.3742922E-03 1.0053766E-02 gauss-seidel spectral radius is 0.9980898 estimated iterations to convergence 182 setup time was (sec) 0.6400000 now iterating at: 13:59:59 rms-change max change #iterations 3.638101 155.7284 at 10iterations 1.476394 54.65606 at 20iterations 0.6019074 21.09804 at 30iterations 0.2453788 7.991295 at 40iterations 9.9924430E-02 3.603586 at 50iterations 4.0939074E-02 1.309864 at 60iterations 1.6678292E-02 0.5150833 at 70iterations 6.8685766E-03 0.2289276 at 80iterations 2.8415041E-03 9.4976425E-02 at 90iterations 1.2120599E-03 4.3571472E-02 at 100iterations 5.4710067E-04 1.9240379E-02 at 110iterations 2.7693884E-04 9.0875626E-03 at 120iterations finished qdiffx linear iterations at : 14:00:14 total time elapsed so far: 8.290000 # loops : 120 mean,max change (kT/e) : 2.7693884E-04 9.0875626E-03 energy calculations done at 8.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.420000 DelPhi exited at 14:00:15 8.424u 0.266s 0:16.82 51.6% 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 Sat Oct 15 2011 at 14:00:15 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: 334 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4449 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: ZN8 820 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 2.302419 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): -17.21500 37.42800 ymin,ymax (A): -33.09100 32.45000 zmin,zma (A): -4.023000 65.55600 x,y,z range (A): 54.64300 65.54100 69.57900 scale (grids/A): 2.302419 object centre (A): 10.10650 -0.3204994 30.76650 number of atom coordinates read : 4449 total number of charged atoms : 4201 net assigned charge : 3.606023 assigned positive charge : 662.1941 centred at (gu) : 91.57233 94.30715 78.95760 assigned negative charge : -658.5922 centred at (gu) : 90.93921 94.46245 79.04065 start vw surface at 0.1100000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 196703 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39498 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 87149 mr = 142362 m= 21527 mr = 67710 m= 3088 mr = 15320 m= 178 mr = 1842 m= 1 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 152 time to turn everything in is 1.070000 number of dielectric boundary points 81358 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 61 iepsmp to db, and charging done at 1.200000 number of grid points assigned charge 33530 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) : 1.534946 object centre at (A) : 10.10650 -0.3204994 30.76650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1593476 0.2625288 midg,1,midg; midg,igrid,midg -0.1075796 -0.3380741 1,midg,midg; igrid,midg,midg -5.6953248E-02 0.1326411 gauss-seidel spectral radius is 0.9991488 estimated iterations to convergence 271 setup time was (sec) 1.380000 now iterating at: 14:00:17 rms-change max change #iterations 9.841455 289.9374 at 10iterations 5.608869 120.3343 at 20iterations 3.169087 67.59725 at 30iterations 1.782852 38.31009 at 40iterations 0.9993295 21.07580 at 50iterations 0.5599114 12.57427 at 60iterations 0.3110926 6.417728 at 70iterations 0.1732616 4.064758 at 80iterations 9.6324712E-02 2.036565 at 90iterations 5.3348709E-02 1.083367 at 100iterations 2.9624565E-02 0.6399364 at 110iterations 1.6397810E-02 0.3364849 at 120iterations 9.1098091E-03 0.1935654 at 130iterations 5.0322637E-03 0.1035709 at 140iterations 2.7944599E-03 5.8303356E-02 at 150iterations 1.5493210E-03 3.0994415E-02 at 160iterations 8.6429092E-04 1.7569542E-02 at 170iterations 4.8602777E-04 1.0320663E-02 at 180iterations finished qdiffx linear iterations at : 14:00:47 total time elapsed so far: 14.87000 # loops : 180 mean,max change (kT/e) : 4.8602777E-04 1.0320663E-02 energy calculations done at 14.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.00000 DelPhi exited at 14:00:48 15.000u 0.317s 0:32.72 46.7% 0+0k 0+0io 0pf+0w