Mon Oct 10 10:40:36 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 Mon Oct 10 2011 at 10:40:36 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: 366 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5043 !!! WARNING: NAP 1619 has a net charge of -2.0000 !!! WARNING: NAP 1620 has a net charge of -2.0000 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: 0.5414696 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): -45.42600 10.69200 ymin,ymax (A): -26.55600 39.19100 zmin,zma (A): -4.230000 58.07200 x,y,z range (A): 56.11800 65.74700 62.30200 scale (grids/A): 0.5414696 object centre (A): -17.36700 6.317501 26.92100 number of atom coordinates read : 5043 total number of charged atoms : 4943 net assigned charge : 7.500004 assigned positive charge : 807.4070 centred at (gu) : 90.45377 90.31628 89.80151 assigned negative charge : -799.9144 centred at (gu) : 90.46246 90.35769 89.84795 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 9718 nv = 96 ne = 84 npr = 98365 no. pairs analyzed = 98365 no. exposed pairs = 6079 no. arc points = 40754 no. surface atoms = 2038 nbur = 3005 mkacc time = 0.2600000 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 = 1.568000 m= 399 mr = 5546 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 51 time to turn everything in is 0.5100000 number of dielectric boundary points 4551 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4088 ## 504 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 12719 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.0108110E-10 -7.4953745E-11 midg,1,midg; midg,igrid,midg 7.4666018E-10 -3.2402660E-11 1,midg,midg; igrid,midg,midg 4.2917775E-10 3.3878012E-10 gauss-seidel spectral radius is 0.9825691 estimated iterations to convergence 62 setup time was (sec) 0.8500000 now iterating at: 10:40:37 rms-change max change #iterations 9.7972609E-02 12.94665 at 10iterations 6.9754883E-03 0.9181662 at 20iterations 1.1517438E-03 0.1663113 at 30iterations 5.3067046E-04 8.0046177E-02 at 40iterations 2.7431000E-04 4.1325569E-02 at 50iterations finished qdiffx linear iterations at : 10:40:41 total time elapsed so far: 4.660000 # loops : 50 mean,max change (kT/e) : 2.7431000E-04 4.1325569E-02 energy calculations done at 4.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.840000 DelPhi exited at 10:40:41 4.842u 0.396s 0:05.54 94.4% 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 Mon Oct 10 2011 at 10:40:41 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: 366 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5043 !!! WARNING: NAP 1619 has a net charge of -2.0000 !!! WARNING: NAP 1620 has a net charge of -2.0000 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: 1.624409 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): -45.42600 10.69200 ymin,ymax (A): -26.55600 39.19100 zmin,zma (A): -4.230000 58.07200 x,y,z range (A): 56.11800 65.74700 62.30200 scale (grids/A): 1.624409 object centre (A): -17.36700 6.317501 26.92100 number of atom coordinates read : 5043 total number of charged atoms : 4943 net assigned charge : 7.500004 assigned positive charge : 807.4070 centred at (gu) : 91.35944 90.94713 89.40237 assigned negative charge : -799.9144 centred at (gu) : 91.38722 91.07305 89.54395 start vw surface at 0.2000000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 110171 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40754 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 36142 mr = 80144 m= 3763 mr = 25717 m= 94 mr = 1895 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 2448 time to turn everything in is 0.9000000 number of dielectric boundary points 42403 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 452 ## 2 charges are in solution ## iepsmp to db, and charging done at 1.060000 number of grid points assigned charge 37809 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) : 0.5414696 object centre at (A) : -17.36700 6.317501 26.92100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5856639E-02 7.4106697E-03 midg,1,midg; midg,igrid,midg -2.5114514E-02 -9.4421180E-03 1,midg,midg; igrid,midg,midg 2.4252957E-02 8.7880921E-03 gauss-seidel spectral radius is 0.9983714 estimated iterations to convergence 197 setup time was (sec) 1.250000 now iterating at: 10:40:43 rms-change max change #iterations 4.703326 271.2603 at 10iterations 2.057826 71.10579 at 20iterations 0.8972210 30.29607 at 30iterations 0.3932780 14.59137 at 40iterations 0.1719812 5.559647 at 50iterations 7.5642303E-02 2.125444 at 60iterations 3.3189941E-02 0.9639435 at 70iterations 1.4656789E-02 0.4292259 at 80iterations 6.5135988E-03 0.2021866 at 90iterations 2.9863133E-03 9.3763351E-02 at 100iterations 1.4654850E-03 5.0624847E-02 at 110iterations 8.2285627E-04 2.8157234E-02 at 120iterations finished qdiffx linear iterations at : 10:40:53 total time elapsed so far: 11.55000 # loops : 120 mean,max change (kT/e) : 8.2285627E-04 2.8157234E-02 energy calculations done at 11.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.72000 DelPhi exited at 10:40:54 11.728u 0.431s 0:12.60 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 Mon Oct 10 2011 at 10:40:54 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: 366 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5043 !!! WARNING: NAP 1619 has a net charge of -2.0000 !!! WARNING: NAP 1620 has a net charge of -2.0000 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: 2.436613 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): -45.42600 10.69200 ymin,ymax (A): -26.55600 39.19100 zmin,zma (A): -4.230000 58.07200 x,y,z range (A): 56.11800 65.74700 62.30200 scale (grids/A): 2.436613 object centre (A): -17.36700 6.317501 26.92100 number of atom coordinates read : 5043 total number of charged atoms : 4943 net assigned charge : 7.500004 assigned positive charge : 807.4070 centred at (gu) : 92.03867 91.42037 89.10312 assigned negative charge : -799.9144 centred at (gu) : 92.08073 91.60945 89.31584 start vw surface at 0.1800000 fill in re-entrant regions at 0.6600000 boundary points on vw surface= 256857 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40754 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 125632 mr = 195379 m= 35987 mr = 101937 m= 5792 mr = 27538 m= 397 mr = 3788 m= 6 mr = 207 m= 0 mr = 0 time to grow re-entrant surface = 1.400000 no. cavity mid-points inaccessible to solvent = 8682 time to turn everything in is 2.210000 number of dielectric boundary points 95822 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 38 iepsmp to db, and charging done at 2.430000 number of grid points assigned charge 39490 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) : 1.624409 object centre at (A) : -17.36700 6.317501 26.92100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1753891 0.1061821 midg,1,midg; midg,igrid,midg -0.4744570 -0.1416577 1,midg,midg; igrid,midg,midg 0.3867549 0.1541951 gauss-seidel spectral radius is 0.9992375 estimated iterations to convergence 286 setup time was (sec) 2.620000 now iterating at: 10:40:57 rms-change max change #iterations 12.12815 359.9056 at 10iterations 7.134647 156.0474 at 20iterations 4.169931 83.96657 at 30iterations 2.424591 51.35400 at 40iterations 1.404624 26.68714 at 50iterations 0.8108220 16.32969 at 60iterations 0.4675974 8.901901 at 70iterations 0.2691452 5.324421 at 80iterations 0.1545988 2.921685 at 90iterations 8.8797882E-02 1.984165 at 100iterations 5.0880849E-02 1.024215 at 110iterations 2.9196292E-02 0.5692406 at 120iterations 1.6758485E-02 0.3106461 at 130iterations 9.6104890E-03 0.1667128 at 140iterations 5.5369409E-03 9.0159416E-02 at 150iterations 3.2302937E-03 5.1747799E-02 at 160iterations 1.9120832E-03 3.3973694E-02 at 170iterations 1.1771726E-03 2.1736145E-02 at 180iterations finished qdiffx linear iterations at : 10:41:14 total time elapsed so far: 19.91000 # loops : 180 mean,max change (kT/e) : 1.1771726E-03 2.1736145E-02 energy calculations done at 19.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.09000 DelPhi exited at 10:41:15 20.095u 0.498s 0:21.03 97.8% 0+0k 0+0io 0pf+0w