Sat Oct 8 18:28:18 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 8 2011 at 18:28:18 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2586 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: PHE 260 has a net charge of 0.5000 !!! WARNING: ZN5 556 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: 0.6226062 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): -32.08400 17.44400 ymin,ymax (A): -23.46000 22.89300 zmin,zma (A): -12.55100 44.62800 x,y,z range (A): 49.52800 46.35300 57.17900 scale (grids/A): 0.6226062 object centre (A): -7.320000 -0.2834997 16.03850 number of atom coordinates read : 2586 total number of charged atoms : 2449 net assigned charge : 4.406008 assigned positive charge : 392.2440 centred at (gu) : 88.58574 89.18517 89.89640 assigned negative charge : -387.8386 centred at (gu) : 88.49319 89.24895 89.76440 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6513 nv = 96 ne = 84 npr = 54199 no. pairs analyzed = 54199 no. exposed pairs = 2921 no. arc points = 20824 no. surface atoms = 991 nbur = 1595 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 319 mr = 3706 m= 1 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 95 time to turn everything in is 0.2900000 number of dielectric boundary points 3087 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2108 ## 204 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8100 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.7906315E-09 1.2908197E-08 midg,1,midg; midg,igrid,midg 1.0091618E-08 -5.3050314E-10 1,midg,midg; igrid,midg,midg -3.8936494E-09 7.6893976E-09 gauss-seidel spectral radius is 0.9866322 estimated iterations to convergence 71 setup time was (sec) 0.5000000 now iterating at: 18:28:19 rms-change max change #iterations 0.1307929 19.80075 at 10iterations 1.2249009E-02 1.914842 at 20iterations 1.1405403E-03 0.1592159 at 30iterations 1.0575650E-04 1.4755249E-02 at 40iterations 9.7739157E-06 1.3074875E-03 at 50iterations finished qdiffx linear iterations at : 18:28:21 total time elapsed so far: 2.920000 # loops : 50 mean,max change (kT/e) : 9.7739157E-06 1.3074875E-03 energy calculations done at 2.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.090000 DelPhi exited at 18:28:22 3.092u 0.137s 0:03.54 90.9% 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 Sat Oct 8 2011 at 18:28:22 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2586 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: PHE 260 has a net charge of 0.5000 !!! WARNING: ZN5 556 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: 1.867819 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): -32.08400 17.44400 ymin,ymax (A): -23.46000 22.89300 zmin,zma (A): -12.55100 44.62800 x,y,z range (A): 49.52800 46.35300 57.17900 scale (grids/A): 1.867819 object centre (A): -7.320000 -0.2834997 16.03850 number of atom coordinates read : 2586 total number of charged atoms : 2449 net assigned charge : 4.406008 assigned positive charge : 392.2440 centred at (gu) : 85.75696 87.55505 89.68859 assigned negative charge : -387.8386 centred at (gu) : 85.47931 87.74672 89.29303 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 70844 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20824 grid for indexing accessible points = 1.400000 m= 25007 mr = 50002 m= 3621 mr = 18647 m= 183 mr = 2319 m= 3 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 5161 time to turn everything in is 0.4900000 number of dielectric boundary points 28617 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 19184 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) : 0.6226062 object centre at (A) : -7.320000 -0.2834997 16.03850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5328597E-02 2.4967428E-02 midg,1,midg; midg,igrid,midg 1.4625145E-02 -9.8069687E-04 1,midg,midg; igrid,midg,midg -2.5487284E-03 3.1727098E-02 gauss-seidel spectral radius is 0.9985741 estimated iterations to convergence 210 setup time was (sec) 0.7500000 now iterating at: 18:28:23 rms-change max change #iterations 4.062860 192.4531 at 10iterations 1.868015 65.86180 at 20iterations 0.8595452 31.58574 at 30iterations 0.3963820 12.51463 at 40iterations 0.1825928 6.265388 at 50iterations 8.4300503E-02 2.685316 at 60iterations 3.8893580E-02 1.209019 at 70iterations 1.7964507E-02 0.5874386 at 80iterations 8.2501639E-03 0.2857094 at 90iterations 3.8035368E-03 0.1261215 at 100iterations 1.7525383E-03 6.2345982E-02 at 110iterations 8.0678193E-04 2.5409698E-02 at 120iterations finished qdiffx linear iterations at : 18:28:29 total time elapsed so far: 6.690000 # loops : 120 mean,max change (kT/e) : 8.0678193E-04 2.5409698E-02 energy calculations done at 6.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.860000 DelPhi exited at 18:28:29 6.863u 0.177s 0:07.31 96.1% 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 8 2011 at 18:28:29 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2586 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: PHE 260 has a net charge of 0.5000 !!! WARNING: ZN5 556 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: 2.801728 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): -32.08400 17.44400 ymin,ymax (A): -23.46000 22.89300 zmin,zma (A): -12.55100 44.62800 x,y,z range (A): 49.52800 46.35300 57.17900 scale (grids/A): 2.801728 object centre (A): -7.320000 -0.2834997 16.03850 number of atom coordinates read : 2586 total number of charged atoms : 2449 net assigned charge : 4.406008 assigned positive charge : 392.2440 centred at (gu) : 83.63537 86.33257 89.53310 assigned negative charge : -387.8386 centred at (gu) : 83.21894 86.62008 88.93949 start vw surface at 0.1600000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 163860 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20824 grid for indexing accessible points = 1.400000 m= 82598 mr = 120678 m= 28077 mr = 68422 m= 6530 mr = 22743 m= 821 mr = 5041 m= 54 mr = 559 m= 1 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.6700001 no. cavity mid-points inaccessible to solvent = 16496 time to turn everything in is 1.210000 number of dielectric boundary points 64473 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.330000 number of grid points assigned charge 19590 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) : 1.867819 object centre at (A) : -7.320000 -0.2834997 16.03850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.1148150E-02 0.3000483 midg,1,midg; midg,igrid,midg 0.1615242 -2.5880482E-02 1,midg,midg; igrid,midg,midg 1.6045386E-02 0.4182936 gauss-seidel spectral radius is 0.9992348 estimated iterations to convergence 285 setup time was (sec) 1.480000 now iterating at: 18:28:31 rms-change max change #iterations 9.488546 374.8143 at 10iterations 5.404688 107.2926 at 20iterations 3.073986 64.51860 at 30iterations 1.747346 36.81581 at 40iterations 0.9926837 17.02556 at 50iterations 0.5619114 10.71731 at 60iterations 0.3202159 6.032772 at 70iterations 0.1814702 3.334236 at 80iterations 0.1032158 1.993111 at 90iterations 5.8565054E-02 1.038785 at 100iterations 3.3296354E-02 0.6470299 at 110iterations 1.8927634E-02 0.3579798 at 120iterations 1.0733374E-02 0.2163992 at 130iterations 6.1088363E-03 0.1146679 at 140iterations 3.4665496E-03 6.3804626E-02 at 150iterations 1.9686136E-03 4.1187286E-02 at 160iterations 1.1234957E-03 2.1438599E-02 at 170iterations 6.3729781E-04 1.2634277E-02 at 180iterations finished qdiffx linear iterations at : 18:28:40 total time elapsed so far: 10.85000 # loops : 180 mean,max change (kT/e) : 6.3729781E-04 1.2634277E-02 energy calculations done at 10.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.03000 DelPhi exited at 18:28:41 11.031u 0.175s 0:11.47 97.6% 0+0k 0+0io 0pf+0w