Tue Oct 11 03:36:00 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 03:36:00 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2169 !!! WARNING: ASL 331 has a net charge of -0.1000 !!! WARNING: HIR 435 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6116313 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): -15.53500 26.71600 ymin,ymax (A): -2.645000 51.87000 zmin,zma (A): 60.31000 118.5150 x,y,z range (A): 42.25100 54.51500 58.20500 scale (grids/A): 0.6116313 object centre (A): 5.590500 24.61250 89.41250 number of atom coordinates read : 2169 total number of charged atoms : 2091 net assigned charge : -5.585979 assigned positive charge : 324.7984 centred at (gu) : 89.19499 89.31230 89.15092 assigned negative charge : -330.3849 centred at (gu) : 89.05649 89.41761 89.17393 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5523 nv = 96 ne = 84 npr = 43755 no. pairs analyzed = 43755 no. exposed pairs = 2745 no. arc points = 19691 no. surface atoms = 929 nbur = 1240 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 249 mr = 2963 m= 3 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 2792 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1883 ## 139 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 6742 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.9131775E-09 -3.7150660E-09 midg,1,midg; midg,igrid,midg 1.3758308E-09 -7.0031856E-09 1,midg,midg; igrid,midg,midg -1.1575359E-08 2.1190127E-09 gauss-seidel spectral radius is 0.9861278 estimated iterations to convergence 70 setup time was (sec) 0.6000000 now iterating at: 03:36:14 rms-change max change #iterations 0.1112898 19.48037 at 10iterations 9.8772896E-03 1.490723 at 20iterations 8.7977003E-04 0.1448865 at 30iterations 7.6779288E-05 1.2105942E-02 at 40iterations 6.8624381E-06 1.1367798E-03 at 50iterations finished qdiffx linear iterations at : 03:36:19 total time elapsed so far: 5.490000 # loops : 50 mean,max change (kT/e) : 6.8624381E-06 1.1367798E-03 energy calculations done at 5.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.660000 DelPhi exited at 03:36:21 5.664u 0.495s 0:21.17 29.0% 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 03:36:21 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2169 !!! WARNING: ASL 331 has a net charge of -0.1000 !!! WARNING: HIR 435 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.834894 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): -15.53500 26.71600 ymin,ymax (A): -2.645000 51.87000 zmin,zma (A): 60.31000 118.5150 x,y,z range (A): 42.25100 54.51500 58.20500 scale (grids/A): 1.834894 object centre (A): 5.590500 24.61250 89.41250 number of atom coordinates read : 2169 total number of charged atoms : 2091 net assigned charge : -5.585979 assigned positive charge : 324.7984 centred at (gu) : 87.58461 87.93665 87.45272 assigned negative charge : -330.3849 centred at (gu) : 87.16941 88.25271 87.52175 start vw surface at 0.1100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 59769 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19691 grid for indexing accessible points = 1.400000 m= 20619 mr = 40717 m= 2850 mr = 15086 m= 89 mr = 1622 m= 0 mr = 17 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 25885 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 111 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 16364 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) : 0.6116313 object centre at (A) : 5.590500 24.61250 89.41250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.4158838E-03 -1.9908296E-02 midg,1,midg; midg,igrid,midg -3.5093836E-02 -4.0491045E-02 1,midg,midg; igrid,midg,midg -8.2379058E-03 1.5532355E-02 gauss-seidel spectral radius is 0.9984900 estimated iterations to convergence 204 setup time was (sec) 0.8200000 now iterating at: 03:36:51 rms-change max change #iterations 3.580321 178.2480 at 10iterations 1.612981 62.62739 at 20iterations 0.7257428 25.92284 at 30iterations 0.3253840 11.88668 at 40iterations 0.1468605 5.019704 at 50iterations 6.6178106E-02 2.355982 at 60iterations 2.9585205E-02 0.9799004 at 70iterations 1.3369875E-02 0.4571304 at 80iterations 6.0274680E-03 0.2019653 at 90iterations 2.7099617E-03 0.1017719 at 100iterations 1.2199308E-03 4.3919563E-02 at 110iterations 5.4939714E-04 2.2888184E-02 at 120iterations finished qdiffx linear iterations at : 03:37:02 total time elapsed so far: 11.16000 # loops : 120 mean,max change (kT/e) : 5.4939714E-04 2.2888184E-02 energy calculations done at 11.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.33000 DelPhi exited at 03:37:03 11.331u 0.642s 0:41.51 28.8% 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 Tue Oct 11 2011 at 03:37:03 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2169 !!! WARNING: ASL 331 has a net charge of -0.1000 !!! WARNING: HIR 435 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.752341 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): -15.53500 26.71600 ymin,ymax (A): -2.645000 51.87000 zmin,zma (A): 60.31000 118.5150 x,y,z range (A): 42.25100 54.51500 58.20500 scale (grids/A): 2.752341 object centre (A): 5.590500 24.61250 89.41250 number of atom coordinates read : 2169 total number of charged atoms : 2091 net assigned charge : -5.585979 assigned positive charge : 324.7984 centred at (gu) : 86.37679 86.90478 86.17896 assigned negative charge : -330.3849 centred at (gu) : 85.75401 87.37911 86.28259 start vw surface at 0.1100000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 138556 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19691 grid for indexing accessible points = 1.400000 m= 67714 mr = 99298 m= 23538 mr = 54959 m= 4807 mr = 18708 m= 442 mr = 3449 m= 22 mr = 263 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.7600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.270000 number of dielectric boundary points 58400 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 16727 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) : 1.834894 object centre at (A) : 5.590500 24.61250 89.41250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.8162466E-02 -0.2613424 midg,1,midg; midg,igrid,midg -0.3337922 -0.4731584 1,midg,midg; igrid,midg,midg -5.8456361E-02 0.2243185 gauss-seidel spectral radius is 0.9992138 estimated iterations to convergence 282 setup time was (sec) 1.610000 now iterating at: 03:37:05 rms-change max change #iterations 8.502786 300.9143 at 10iterations 4.820949 114.7680 at 20iterations 2.735074 58.33374 at 30iterations 1.540499 33.34609 at 40iterations 0.8696822 19.97186 at 50iterations 0.4904112 12.06793 at 60iterations 0.2762195 5.632408 at 70iterations 0.1559590 3.055733 at 80iterations 8.7886952E-02 1.795567 at 90iterations 4.9380936E-02 1.010756 at 100iterations 2.7835445E-02 0.5279655 at 110iterations 1.5690863E-02 0.3184017 at 120iterations 8.8064456E-03 0.1810284 at 130iterations 4.9797455E-03 0.1060700 at 140iterations 2.8018062E-03 5.2970886E-02 at 150iterations 1.5799062E-03 3.1578064E-02 at 160iterations 8.9076255E-04 1.7524719E-02 at 170iterations 5.0193543E-04 1.0299683E-02 at 180iterations finished qdiffx linear iterations at : 03:37:24 total time elapsed so far: 18.98000 # loops : 180 mean,max change (kT/e) : 5.0193543E-04 1.0299683E-02 energy calculations done at 18.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.16000 DelPhi exited at 03:37:24 19.167u 0.758s 0:21.33 93.3% 0+0k 0+0io 0pf+0w