Tue Oct 11 06:14:26 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 Tue Oct 11 2011 at 06:14:26 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2046 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 0.7041278 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): 16.38800 63.51200 ymin,ymax (A): -3.490000 32.93500 zmin,zma (A): 21.90500 72.46400 x,y,z range (A): 47.12400 36.42500 50.55901 scale (grids/A): 0.7041278 object centre (A): 39.95000 14.72250 47.18450 number of atom coordinates read : 2046 total number of charged atoms : 1913 net assigned charge : 5.420006 assigned positive charge : 310.4040 centred at (gu) : 90.84708 89.94818 89.07918 assigned negative charge : -304.9842 centred at (gu) : 90.95322 90.01125 89.04662 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6898 nv = 96 ne = 84 npr = 41298 no. pairs analyzed = 41298 no. exposed pairs = 2461 no. arc points = 17005 no. surface atoms = 839 nbur = 1207 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 466 mr = 3948 m= 5 mr = 113 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3308 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1555 ## 131 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7629 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.3405463E-08 4.8138308E-08 midg,1,midg; midg,igrid,midg 7.1644223E-08 1.4275287E-08 1,midg,midg; igrid,midg,midg 7.6284323E-08 -6.7203638E-09 gauss-seidel spectral radius is 0.9894846 estimated iterations to convergence 79 setup time was (sec) 0.5200000 now iterating at: 06:14:27 rms-change max change #iterations 0.1937088 25.66092 at 10iterations 2.4339091E-02 3.698654 at 20iterations 3.0333719E-03 0.4084530 at 30iterations 4.5805302E-04 5.9770584E-02 at 40iterations 1.0079850E-04 1.3870239E-02 at 50iterations finished qdiffx linear iterations at : 06:14:30 total time elapsed so far: 3.380000 # loops : 50 mean,max change (kT/e) : 1.0079850E-04 1.3870239E-02 energy calculations done at 3.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 06:14:31 3.589u 0.219s 0:04.47 84.7% 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 Tue Oct 11 2011 at 06:14:31 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2046 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 2.112383 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): 16.38800 63.51200 ymin,ymax (A): -3.490000 32.93500 zmin,zma (A): 21.90500 72.46400 x,y,z range (A): 47.12400 36.42500 50.55901 scale (grids/A): 2.112383 object centre (A): 39.95000 14.72250 47.18450 number of atom coordinates read : 2046 total number of charged atoms : 1913 net assigned charge : 5.420006 assigned positive charge : 310.4040 centred at (gu) : 92.54129 89.84444 87.23745 assigned negative charge : -304.9842 centred at (gu) : 92.85976 90.03389 87.13973 start vw surface at 0.1500000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 73249 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17005 grid for indexing accessible points = 1.400000 m= 29994 mr = 52032 m= 6121 mr = 22989 m= 611 mr = 4173 m= 16 mr = 323 m= 0 mr = 4 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6500000 number of dielectric boundary points 30470 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 57 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 15157 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) : 0.7041278 object centre at (A) : 39.95000 14.72250 47.18450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1003067E-02 3.4471646E-02 midg,1,midg; midg,igrid,midg 2.3808772E-02 7.5605772E-03 1,midg,midg; igrid,midg,midg 2.7109828E-02 2.2626366E-02 gauss-seidel spectral radius is 0.9988173 estimated iterations to convergence 230 setup time was (sec) 0.9600000 now iterating at: 06:14:32 rms-change max change #iterations 4.532161 181.5002 at 10iterations 2.242811 77.61089 at 20iterations 1.105534 37.32251 at 30iterations 0.5462434 16.94570 at 40iterations 0.2703473 8.398067 at 50iterations 0.1336562 4.116827 at 60iterations 6.6218182E-02 2.094864 at 70iterations 3.2739624E-02 1.055502 at 80iterations 1.6319484E-02 0.5518808 at 90iterations 8.1306221E-03 0.2584257 at 100iterations 4.0557883E-03 0.1359529 at 110iterations 2.0571775E-03 6.3045502E-02 at 120iterations finished qdiffx linear iterations at : 06:14:39 total time elapsed so far: 7.950000 # loops : 120 mean,max change (kT/e) : 2.0571775E-03 6.3045502E-02 energy calculations done at 7.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.140000 DelPhi exited at 06:14:39 8.147u 0.236s 0:08.68 96.4% 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 Tue Oct 11 2011 at 06:14:39 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2046 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 3.168575 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): 16.38800 63.51200 ymin,ymax (A): -3.490000 32.93500 zmin,zma (A): 21.90500 72.46400 x,y,z range (A): 47.12400 36.42500 50.55901 scale (grids/A): 3.168575 object centre (A): 39.95000 14.72250 47.18450 number of atom coordinates read : 2046 total number of charged atoms : 1913 net assigned charge : 5.420006 assigned positive charge : 310.4040 centred at (gu) : 93.81194 89.76668 85.85617 assigned negative charge : -304.9842 centred at (gu) : 94.28960 90.05085 85.70962 start vw surface at 0.1400000 fill in re-entrant regions at 0.8300000 boundary points on vw surface= 168713 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17005 grid for indexing accessible points = 1.400000 m= 92928 mr = 125270 m= 38897 mr = 77673 m= 11603 mr = 32254 m= 2376 mr = 9122 m= 283 mr = 1761 m= 9 mr = 171 m= 0 mr = 4 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.860000 number of dielectric boundary points 68554 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.010000 number of grid points assigned charge 15300 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) : 2.112383 object centre at (A) : 39.95000 14.72250 47.18450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2513186 6.4565212E-02 midg,1,midg; midg,igrid,midg 0.1977088 5.9593428E-02 1,midg,midg; igrid,midg,midg 0.2762960 0.4259337 gauss-seidel spectral radius is 0.9992932 estimated iterations to convergence 297 setup time was (sec) 2.210000 now iterating at: 06:14:42 rms-change max change #iterations 10.08198 328.3250 at 10iterations 5.948711 122.8419 at 20iterations 3.506396 78.82802 at 30iterations 2.061194 41.58942 at 40iterations 1.207957 23.76205 at 50iterations 0.7091039 13.41284 at 60iterations 0.4158262 8.132399 at 70iterations 0.2429648 4.768564 at 80iterations 0.1424343 2.685745 at 90iterations 8.3319724E-02 1.472321 at 100iterations 4.8741244E-02 0.8893242 at 110iterations 2.8605336E-02 0.5113211 at 120iterations 1.6815703E-02 0.3151150 at 130iterations 9.9597936E-03 0.2100182 at 140iterations 6.0018906E-03 0.1085401 at 150iterations 3.6970356E-03 7.3532104E-02 at 160iterations 2.3689175E-03 4.2087555E-02 at 170iterations 1.6012846E-03 3.0060053E-02 at 180iterations finished qdiffx linear iterations at : 06:14:53 total time elapsed so far: 13.43000 # loops : 180 mean,max change (kT/e) : 1.6012846E-03 3.0060053E-02 energy calculations done at 13.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.64000 DelPhi exited at 06:14:54 13.640u 0.246s 0:14.40 96.3% 0+0k 0+0io 0pf+0w