Thu Jan 19 13:33:47 PST 2012 #!/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 Thu Jan 19 2012 at 13:33:48 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: 343 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6831 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 1105 has a net charge of -4.0000 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: 0.4239357 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): -10.68700 73.28800 ymin,ymax (A): -56.08100 11.58800 zmin,zma (A): -102.3920 -22.85100 x,y,z range (A): 83.97501 67.66900 79.54100 scale (grids/A): 0.4239357 object centre (A): 31.30050 -22.24650 -62.62150 number of atom coordinates read : 6831 total number of charged atoms : 6661 net assigned charge : 1.200043 assigned positive charge : 1045.992 centred at (gu) : 88.24968 89.61737 89.79694 assigned negative charge : -1044.801 centred at (gu) : 88.17072 89.53683 89.73754 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7532 nv = 96 ne = 84 npr = 131507 no. pairs analyzed = 131507 no. exposed pairs = 9525 no. arc points = 65353 no. surface atoms = 3148 nbur = 3683 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 = 1.960000 m= 198 mr = 3381 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 4349 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5375 ## 1174 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 10409 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.5183924E-12 2.6469773E-12 midg,1,midg; midg,igrid,midg -3.7321556E-12 3.2997910E-12 1,midg,midg; igrid,midg,midg -5.6771645E-12 2.1120317E-12 gauss-seidel spectral radius is 0.9717934 estimated iterations to convergence 50 setup time was (sec) 0.6400000 now iterating at: 13:33:49 rms-change max change #iterations 2.7865801E-02 4.997040 at 10iterations 1.2470890E-03 0.1981125 at 20iterations 3.1474425E-04 3.8740158E-02 at 30iterations 1.1589552E-04 1.4616013E-02 at 40iterations 4.3234348E-05 5.6056976E-03 at 50iterations finished qdiffx linear iterations at : 13:33:56 total time elapsed so far: 3.900000 # loops : 50 mean,max change (kT/e) : 4.3234348E-05 5.6056976E-03 energy calculations done at 3.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.030000 DelPhi exited at 13:33:57 4.038u 0.179s 0:09.06 46.3% 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 Thu Jan 19 2012 at 13:33:57 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: 343 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6831 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 1105 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.271807 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): -10.68700 73.28800 ymin,ymax (A): -56.08100 11.58800 zmin,zma (A): -102.3920 -22.85100 x,y,z range (A): 83.97501 67.66900 79.54100 scale (grids/A): 1.271807 object centre (A): 31.30050 -22.24650 -62.62150 number of atom coordinates read : 6831 total number of charged atoms : 6661 net assigned charge : 1.200043 assigned positive charge : 1045.992 centred at (gu) : 84.74706 88.85072 89.38914 assigned negative charge : -1044.801 centred at (gu) : 84.51170 88.61002 89.21197 start vw surface at 0.1700000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 88382 reading accessible surface arcs data from file ARCDAT no. of arc points read = 65353 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.848000 m= 21307 mr = 57005 m= 1000 mr = 12493 m= 7 mr = 186 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 210 time to turn everything in is 0.4800000 number of dielectric boundary points 41012 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1276 ## 62 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 45731 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) : 0.4239357 object centre at (A) : 31.30050 -22.24650 -62.62150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8699606E-03 4.3233186E-03 midg,1,midg; midg,igrid,midg -2.7906159E-03 2.1353483E-03 1,midg,midg; igrid,midg,midg -1.1787224E-02 1.6583543E-03 gauss-seidel spectral radius is 0.9973489 estimated iterations to convergence 155 setup time was (sec) 0.7200000 now iterating at: 13:34:02 rms-change max change #iterations 2.976995 129.3656 at 10iterations 1.031928 41.76322 at 20iterations 0.3576736 13.35479 at 30iterations 0.1246367 4.869236 at 40iterations 4.3290354E-02 1.532856 at 50iterations 1.5167686E-02 0.5501204 at 60iterations 5.3266906E-03 0.2073579 at 70iterations 1.9268533E-03 6.7344666E-02 at 80iterations 7.5798726E-04 2.5913239E-02 at 90iterations 3.6041468E-04 1.2840271E-02 at 100iterations 2.1195864E-04 7.0695877E-03 at 110iterations 1.3980070E-04 3.9844513E-03 at 120iterations finished qdiffx linear iterations at : 13:34:26 total time elapsed so far: 8.700000 # loops : 120 mean,max change (kT/e) : 1.3980070E-04 3.9844513E-03 energy calculations done at 8.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.830000 DelPhi exited at 13:34:26 8.830u 0.221s 0:29.38 30.8% 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 Thu Jan 19 2012 at 13:34:27 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: 343 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6831 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 1105 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.907710 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): -10.68700 73.28800 ymin,ymax (A): -56.08100 11.58800 zmin,zma (A): -102.3920 -22.85100 x,y,z range (A): 83.97501 67.66900 79.54100 scale (grids/A): 1.907710 object centre (A): 31.30050 -22.24650 -62.62150 number of atom coordinates read : 6831 total number of charged atoms : 6661 net assigned charge : 1.200043 assigned positive charge : 1045.992 centred at (gu) : 82.12000 88.27560 89.08304 assigned negative charge : -1044.801 centred at (gu) : 81.76741 87.91486 88.81793 start vw surface at 0.1800000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 206722 reading accessible surface arcs data from file ARCDAT no. of arc points read = 65353 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.820000 m= 82662 mr = 142585 m= 14620 mr = 60252 m= 921 mr = 9148 m= 7 mr = 311 m= 0 mr = 0 time to grow re-entrant surface = 0.6300000 no. cavity mid-points inaccessible to solvent = 799 time to turn everything in is 1.110000 number of dielectric boundary points 92636 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 377 ## 1 charges are in solution ## iepsmp to db, and charging done at 1.230000 number of grid points assigned charge 52477 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) : 1.271807 object centre at (A) : 31.30050 -22.24650 -62.62150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1365460 9.9797264E-02 midg,1,midg; midg,igrid,midg -6.8552181E-02 5.8885723E-02 1,midg,midg; igrid,midg,midg -0.4340941 8.3119474E-02 gauss-seidel spectral radius is 0.9989743 estimated iterations to convergence 247 setup time was (sec) 1.390000 now iterating at: 13:34:29 rms-change max change #iterations 9.391904 330.8596 at 10iterations 5.111269 132.1712 at 20iterations 2.749958 68.67830 at 30iterations 1.467894 39.46030 at 40iterations 0.7795867 23.87266 at 50iterations 0.4124830 12.42345 at 60iterations 0.2172869 5.261740 at 70iterations 0.1143083 2.502270 at 80iterations 6.0047310E-02 1.394018 at 90iterations 3.1493176E-02 0.7043800 at 100iterations 1.6508227E-02 0.3410754 at 110iterations 8.6150253E-03 0.1838589 at 120iterations 4.5037237E-03 9.8941803E-02 at 130iterations 2.3566277E-03 5.3630829E-02 at 140iterations 1.2293913E-03 2.7144730E-02 at 150iterations 6.4186996E-04 1.3740540E-02 at 160iterations 3.3549702E-04 7.3356628E-03 at 170iterations 1.7510429E-04 3.6120415E-03 at 180iterations finished qdiffx linear iterations at : 13:35:07 total time elapsed so far: 14.51000 # loops : 180 mean,max change (kT/e) : 1.7510429E-04 3.6120415E-03 energy calculations done at 14.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.66000 DelPhi exited at 13:35:08 14.657u 0.291s 0:41.37 36.1% 0+0k 0+0io 0pf+0w