Mon Oct 10 19:36:41 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 19:36:41 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2203 !!! WARNING: GLM 33 has a net charge of -0.0940 !!! WARNING: SEP 67 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6395516 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): -35.89600 2.145000 ymin,ymax (A): 31.91200 87.57600 zmin,zma (A): -24.56000 24.92100 x,y,z range (A): 38.04100 55.66400 49.48100 scale (grids/A): 0.6395516 object centre (A): -16.87550 59.74400 0.1805000 number of atom coordinates read : 2203 total number of charged atoms : 2123 net assigned charge : -2.568997 assigned positive charge : 324.1185 centred at (gu) : 88.90005 91.87962 89.82812 assigned negative charge : -326.6879 centred at (gu) : 88.87536 91.84681 89.87508 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6109 nv = 96 ne = 84 npr = 44374 no. pairs analyzed = 44374 no. exposed pairs = 2863 no. arc points = 20222 no. surface atoms = 966 nbur = 1237 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 392 mr = 3288 m= 4 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.2800000 number of dielectric boundary points 3152 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1929 ## 176 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7400 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.2958362E-10 -7.9770821E-09 midg,1,midg; midg,igrid,midg -4.6496593E-09 -7.2739714E-10 1,midg,midg; igrid,midg,midg -7.7185716E-09 -1.0938151E-09 gauss-seidel spectral radius is 0.9873030 estimated iterations to convergence 73 setup time was (sec) 0.5500000 now iterating at: 19:36:42 rms-change max change #iterations 0.1340124 25.09880 at 10iterations 1.3021890E-02 2.011742 at 20iterations 1.2607679E-03 0.1918755 at 30iterations 1.2719628E-04 1.8827438E-02 at 40iterations 1.2524191E-05 1.7318726E-03 at 50iterations finished qdiffx linear iterations at : 19:36:45 total time elapsed so far: 3.370000 # loops : 50 mean,max change (kT/e) : 1.2524191E-05 1.7318726E-03 energy calculations done at 3.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 19:36:45 3.562u 0.187s 0:04.11 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 Mon Oct 10 2011 at 19:36:45 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2203 !!! WARNING: GLM 33 has a net charge of -0.0940 !!! WARNING: SEP 67 has a net charge of -0.4750 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: 1.918655 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): -35.89600 2.145000 ymin,ymax (A): 31.91200 87.57600 zmin,zma (A): -24.56000 24.92100 x,y,z range (A): 38.04100 55.66400 49.48100 scale (grids/A): 1.918655 object centre (A): -16.87550 59.74400 0.1805000 number of atom coordinates read : 2203 total number of charged atoms : 2123 net assigned charge : -2.568997 assigned positive charge : 324.1185 centred at (gu) : 86.70004 95.63833 89.48423 assigned negative charge : -326.6879 centred at (gu) : 86.62599 95.54037 89.62507 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 65849 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20222 grid for indexing accessible points = 1.400000 m= 24609 mr = 45144 m= 4669 mr = 18050 m= 362 mr = 3059 m= 5 mr = 169 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 665 time to turn everything in is 0.5400000 number of dielectric boundary points 29072 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 111 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 16748 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) : 0.6395516 object centre at (A) : -16.87550 59.74400 0.1805000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.4783221E-03 -2.7981922E-02 midg,1,midg; midg,igrid,midg 7.8319423E-03 -4.1723721E-02 1,midg,midg; igrid,midg,midg -1.4499298E-02 1.0747945E-02 gauss-seidel spectral radius is 0.9986194 estimated iterations to convergence 213 setup time was (sec) 0.8600000 now iterating at: 19:36:46 rms-change max change #iterations 3.921273 156.4003 at 10iterations 1.826160 67.80538 at 20iterations 0.8530635 31.53026 at 30iterations 0.3986459 15.81462 at 40iterations 0.1857809 6.551569 at 50iterations 8.6627498E-02 3.181026 at 60iterations 4.0600482E-02 1.380745 at 70iterations 1.8869964E-02 0.6293259 at 80iterations 8.8174492E-03 0.2980056 at 90iterations 4.1076695E-03 0.1409676 at 100iterations 1.9203326E-03 6.3393593E-02 at 110iterations 9.0148498E-04 2.9282570E-02 at 120iterations finished qdiffx linear iterations at : 19:36:53 total time elapsed so far: 7.850000 # loops : 120 mean,max change (kT/e) : 9.0148498E-04 2.9282570E-02 energy calculations done at 7.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.050000 DelPhi exited at 19:36:54 8.054u 0.198s 0:08.63 95.4% 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 19:36:54 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2203 !!! WARNING: GLM 33 has a net charge of -0.0940 !!! WARNING: SEP 67 has a net charge of -0.4750 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: 2.877982 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): -35.89600 2.145000 ymin,ymax (A): 31.91200 87.57600 zmin,zma (A): -24.56000 24.92100 x,y,z range (A): 38.04100 55.66400 49.48100 scale (grids/A): 2.877982 object centre (A): -16.87550 59.74400 0.1805000 number of atom coordinates read : 2203 total number of charged atoms : 2123 net assigned charge : -2.568997 assigned positive charge : 324.1185 centred at (gu) : 85.04996 98.45746 89.22615 assigned negative charge : -326.6879 centred at (gu) : 84.93900 98.31053 89.43777 start vw surface at 0.1600000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 152340 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20222 grid for indexing accessible points = 1.400000 m= 77435 mr = 109713 m= 30390 mr = 62856 m= 8553 mr = 24453 m= 1570 mr = 6653 m= 126 mr = 1151 m= 0 mr = 67 time to grow re-entrant surface = 0.7699999 no. cavity mid-points inaccessible to solvent = 2075 time to turn everything in is 1.330000 number of dielectric boundary points 65521 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.490000 number of grid points assigned charge 16984 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) : 1.918655 object centre at (A) : -16.87550 59.74400 0.1805000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.9772967E-02 -0.2366611 midg,1,midg; midg,igrid,midg 0.2944754 -0.8763977 1,midg,midg; igrid,midg,midg -0.1967808 0.1393850 gauss-seidel spectral radius is 0.9992522 estimated iterations to convergence 289 setup time was (sec) 1.670000 now iterating at: 19:36:56 rms-change max change #iterations 9.167520 340.9069 at 10iterations 5.317201 117.3836 at 20iterations 3.063020 63.05123 at 30iterations 1.771908 36.36565 at 40iterations 1.015822 20.45536 at 50iterations 0.5870902 10.81837 at 60iterations 0.3366586 6.808085 at 70iterations 0.1936712 3.505549 at 80iterations 0.1107680 2.119118 at 90iterations 6.3463278E-02 1.302639 at 100iterations 3.6403432E-02 0.7245569 at 110iterations 2.0927224E-02 0.3933046 at 120iterations 1.1974487E-02 0.2527428 at 130iterations 6.8622367E-03 0.1361237 at 140iterations 3.9241081E-03 7.1516037E-02 at 150iterations 2.2484222E-03 4.5171738E-02 at 160iterations 1.2873731E-03 2.3250580E-02 at 170iterations 7.3736999E-04 1.3583183E-02 at 180iterations finished qdiffx linear iterations at : 19:37:07 total time elapsed so far: 12.88000 # loops : 180 mean,max change (kT/e) : 7.3736999E-04 1.3583183E-02 energy calculations done at 12.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.08000 DelPhi exited at 19:37:08 13.085u 0.247s 0:14.00 95.1% 0+0k 0+0io 0pf+0w