Sat Oct 15 11:46:22 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 11:46:22 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2280 !!! WARNING: HIT 84 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6593203 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): 13.98800 67.98300 ymin,ymax (A): -21.99300 30.02200 zmin,zma (A): -33.31200 9.244000 x,y,z range (A): 53.99500 52.01500 42.55600 scale (grids/A): 0.6593203 object centre (A): 40.98550 4.014500 -12.03400 number of atom coordinates read : 2280 total number of charged atoms : 2146 net assigned charge : 11.51402 assigned positive charge : 334.0996 centred at (gu) : 89.33286 88.43681 88.64809 assigned negative charge : -322.5862 centred at (gu) : 89.29591 88.42809 88.73370 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6977 nv = 96 ne = 84 npr = 44815 no. pairs analyzed = 44815 no. exposed pairs = 3161 no. arc points = 22746 no. surface atoms = 1050 nbur = 1230 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 438 mr = 3558 m= 2 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3805 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2052 ## 175 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 7883 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.5648577E-08 1.1299381E-08 midg,1,midg; midg,igrid,midg 3.7101763E-08 2.1869395E-08 1,midg,midg; igrid,midg,midg 2.5680626E-08 3.0050369E-08 gauss-seidel spectral radius is 0.9880608 estimated iterations to convergence 75 setup time was (sec) 0.4300000 now iterating at: 11:46:22 rms-change max change #iterations 0.1559351 22.40982 at 10iterations 1.6235698E-02 2.190258 at 20iterations 1.8069602E-03 0.2407541 at 30iterations 2.4268629E-04 3.6399841E-02 at 40iterations 4.7210589E-05 8.8310242E-03 at 50iterations finished qdiffx linear iterations at : 11:46:26 total time elapsed so far: 3.850000 # loops : 50 mean,max change (kT/e) : 4.7210589E-05 8.8310242E-03 energy calculations done at 3.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.990000 DelPhi exited at 11:46:27 3.989u 0.249s 0:05.05 83.5% 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 11:46:27 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2280 !!! WARNING: HIT 84 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.977961 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): 13.98800 67.98300 ymin,ymax (A): -21.99300 30.02200 zmin,zma (A): -33.31200 9.244000 x,y,z range (A): 53.99500 52.01500 42.55600 scale (grids/A): 1.977961 object centre (A): 40.98550 4.014500 -12.03400 number of atom coordinates read : 2280 total number of charged atoms : 2146 net assigned charge : 11.51402 assigned positive charge : 334.0996 centred at (gu) : 87.99850 85.31026 85.94413 assigned negative charge : -322.5862 centred at (gu) : 87.88770 85.28449 86.20098 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 72831 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22746 grid for indexing accessible points = 1.400000 m= 27492 mr = 47834 m= 5138 mr = 19752 m= 416 mr = 3181 m= 13 mr = 187 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 34936 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 131 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 16987 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) : 0.6593203 object centre at (A) : 40.98550 4.014500 -12.03400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.6413159E-02 -3.1507658E-03 midg,1,midg; midg,igrid,midg 2.8702136E-02 4.1818872E-02 1,midg,midg; igrid,midg,midg 5.9197497E-02 5.4848474E-02 gauss-seidel spectral radius is 0.9987118 estimated iterations to convergence 221 setup time was (sec) 0.6600000 now iterating at: 11:46:28 rms-change max change #iterations 4.100694 184.5755 at 10iterations 1.965153 66.12761 at 20iterations 0.9360015 33.32612 at 30iterations 0.4474245 13.54894 at 40iterations 0.2135459 7.123230 at 50iterations 0.1019063 3.139006 at 60iterations 4.8705991E-02 1.537933 at 70iterations 2.3304578E-02 0.8230152 at 80iterations 1.1123359E-02 0.3585014 at 90iterations 5.3558904E-03 0.1629314 at 100iterations 2.5770376E-03 8.9603424E-02 at 110iterations 1.2464850E-03 4.1004181E-02 at 120iterations finished qdiffx linear iterations at : 11:46:42 total time elapsed so far: 9.230000 # loops : 120 mean,max change (kT/e) : 1.2464850E-03 4.1004181E-02 energy calculations done at 9.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.360000 DelPhi exited at 11:46:43 9.365u 0.289s 0:15.76 61.1% 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 Sat Oct 15 2011 at 11:46:43 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2280 !!! WARNING: HIT 84 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.966941 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): 13.98800 67.98300 ymin,ymax (A): -21.99300 30.02200 zmin,zma (A): -33.31200 9.244000 x,y,z range (A): 53.99500 52.01500 42.55600 scale (grids/A): 2.966941 object centre (A): 40.98550 4.014500 -12.03400 number of atom coordinates read : 2280 total number of charged atoms : 2146 net assigned charge : 11.51402 assigned positive charge : 334.0996 centred at (gu) : 86.99784 82.96533 83.91613 assigned negative charge : -322.5862 centred at (gu) : 86.83162 82.92673 84.30139 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 167995 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22746 grid for indexing accessible points = 1.400000 m= 85363 mr = 116445 m= 34141 mr = 68176 m= 9628 mr = 27127 m= 1729 mr = 7142 m= 174 mr = 1226 m= 8 mr = 98 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.050000 number of dielectric boundary points 78824 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 17167 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) : 1.977961 object centre at (A) : 40.98550 4.014500 -12.03400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3084616 -3.0552631E-02 midg,1,midg; midg,igrid,midg 0.3134513 0.5834165 1,midg,midg; igrid,midg,midg 0.4858260 0.5258374 gauss-seidel spectral radius is 0.9992904 estimated iterations to convergence 296 setup time was (sec) 1.360000 now iterating at: 11:46:44 rms-change max change #iterations 9.779646 426.6855 at 10iterations 5.815840 157.1444 at 20iterations 3.455283 73.75571 at 30iterations 2.031967 42.46620 at 40iterations 1.193405 27.78835 at 50iterations 0.6996685 13.60858 at 60iterations 0.4103227 7.700165 at 70iterations 0.2395706 4.698363 at 80iterations 0.1397061 2.739231 at 90iterations 8.1613354E-02 1.511771 at 100iterations 4.7626548E-02 0.8368440 at 110iterations 2.7702607E-02 0.5492287 at 120iterations 1.6154632E-02 0.2889013 at 130iterations 9.4151292E-03 0.1804218 at 140iterations 5.4846164E-03 0.1126773 at 150iterations 3.1954856E-03 6.1405182E-02 at 160iterations 1.8702451E-03 3.2558441E-02 at 170iterations 1.0990844E-03 2.1224022E-02 at 180iterations finished qdiffx linear iterations at : 11:47:00 total time elapsed so far: 15.66000 # loops : 180 mean,max change (kT/e) : 1.0990844E-03 2.1224022E-02 energy calculations done at 15.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.80000 DelPhi exited at 11:47:01 15.798u 0.344s 0:18.20 88.6% 0+0k 0+0io 0pf+0w