Sat Oct 15 11:34:25 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 11:34:25 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2002 !!! WARNING: HIR 237 has a net charge of 0.5140 !!! WARNING: GLM 283 has a net charge of -0.0940 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: 0.6730442 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): 6.862000 59.75600 ymin,ymax (A): 77.20100 124.0480 zmin,zma (A): -7.395000 33.63900 x,y,z range (A): 52.89400 46.84700 41.03400 scale (grids/A): 0.6730442 object centre (A): 33.30900 100.6245 13.12200 number of atom coordinates read : 2002 total number of charged atoms : 1867 net assigned charge : -7.9996467E-02 assigned positive charge : 300.0248 centred at (gu) : 88.21056 90.22435 90.99173 assigned negative charge : -300.1049 centred at (gu) : 88.32854 90.20373 90.93792 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6226 nv = 96 ne = 84 npr = 40029 no. pairs analyzed = 40029 no. exposed pairs = 2582 no. arc points = 17935 no. surface atoms = 877 nbur = 1125 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 403 mr = 3432 m= 4 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 3148 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1630 ## 149 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7033 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0058018E-08 1.2830005E-08 midg,1,midg; midg,igrid,midg -5.0374234E-09 3.6136698E-09 1,midg,midg; igrid,midg,midg 3.4652931E-08 -1.8090823E-08 gauss-seidel spectral radius is 0.9885026 estimated iterations to convergence 76 setup time was (sec) 0.5800000 now iterating at: 11:34:26 rms-change max change #iterations 0.1622720 24.68767 at 10iterations 1.8639298E-02 2.727394 at 20iterations 3.1037235E-03 0.5052490 at 30iterations 9.8358188E-04 0.1804199 at 40iterations 3.8452569E-04 6.8855286E-02 at 50iterations finished qdiffx linear iterations at : 11:34:30 total time elapsed so far: 5.030000 # loops : 50 mean,max change (kT/e) : 3.8452569E-04 6.8855286E-02 energy calculations done at 5.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.200000 DelPhi exited at 11:34:31 5.202u 0.472s 0:06.01 94.3% 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 11:34:31 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2002 !!! WARNING: HIR 237 has a net charge of 0.5140 !!! WARNING: GLM 283 has a net charge of -0.0940 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: 2.019133 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): 6.862000 59.75600 ymin,ymax (A): 77.20100 124.0480 zmin,zma (A): -7.395000 33.63900 x,y,z range (A): 52.89400 46.84700 41.03400 scale (grids/A): 2.019133 object centre (A): 33.30900 100.6245 13.12200 number of atom coordinates read : 2002 total number of charged atoms : 1867 net assigned charge : -7.9996467E-02 assigned positive charge : 300.0248 centred at (gu) : 84.63148 90.67263 92.97486 assigned negative charge : -300.1049 centred at (gu) : 84.98560 90.61101 92.81359 start vw surface at 0.1100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 66120 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17935 grid for indexing accessible points = 1.400000 m= 25710 mr = 45694 m= 4749 mr = 18930 m= 340 mr = 3037 m= 7 mr = 137 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 29128 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 83 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 14782 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) : 0.6730442 object centre at (A) : 33.30900 100.6245 13.12200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.4687761E-03 1.0887332E-02 midg,1,midg; midg,igrid,midg 3.6489812E-03 2.2144798E-02 1,midg,midg; igrid,midg,midg -2.0421196E-02 -3.1013627E-02 gauss-seidel spectral radius is 0.9987206 estimated iterations to convergence 221 setup time was (sec) 0.9100000 now iterating at: 11:34:32 rms-change max change #iterations 4.160578 183.9841 at 10iterations 2.000838 65.72726 at 20iterations 0.9606014 33.62596 at 30iterations 0.4630191 16.46573 at 40iterations 0.2227448 7.155327 at 50iterations 0.1069262 4.072056 at 60iterations 5.1829327E-02 1.736111 at 70iterations 2.5273236E-02 0.8213463 at 80iterations 1.2545584E-02 0.4155674 at 90iterations 6.4342194E-03 0.2436905 at 100iterations 3.5238836E-03 0.1291351 at 110iterations 2.1163626E-03 8.3663940E-02 at 120iterations finished qdiffx linear iterations at : 11:34:44 total time elapsed so far: 12.51000 # loops : 120 mean,max change (kT/e) : 2.1163626E-03 8.3663940E-02 energy calculations done at 12.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.68000 DelPhi exited at 11:34:44 12.680u 0.534s 0:13.57 97.3% 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 11:34:44 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2002 !!! WARNING: HIR 237 has a net charge of 0.5140 !!! WARNING: GLM 283 has a net charge of -0.0940 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: 3.028699 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): 6.862000 59.75600 ymin,ymax (A): 77.20100 124.0480 zmin,zma (A): -7.395000 33.63900 x,y,z range (A): 52.89400 46.84700 41.03400 scale (grids/A): 3.028699 object centre (A): 33.30900 100.6245 13.12200 number of atom coordinates read : 2002 total number of charged atoms : 1867 net assigned charge : -7.9996467E-02 assigned positive charge : 300.0248 centred at (gu) : 81.94723 91.00899 94.46226 assigned negative charge : -300.1049 centred at (gu) : 82.47829 90.91644 94.22038 start vw surface at 0.1100000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 152620 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17935 grid for indexing accessible points = 1.400000 m= 80454 mr = 110538 m= 31950 mr = 65898 m= 8876 mr = 25684 m= 1508 mr = 6712 m= 125 mr = 1034 m= 0 mr = 57 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.550000 number of dielectric boundary points 65610 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.710000 number of grid points assigned charge 14936 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) : 2.019133 object centre at (A) : 33.30900 100.6245 13.12200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.8520119E-02 0.1226983 midg,1,midg; midg,igrid,midg -6.1117020E-02 0.1879930 1,midg,midg; igrid,midg,midg -0.2778131 -0.2060852 gauss-seidel spectral radius is 0.9992748 estimated iterations to convergence 293 setup time was (sec) 1.940000 now iterating at: 11:34:47 rms-change max change #iterations 9.704977 347.4405 at 10iterations 5.772984 152.7240 at 20iterations 3.400426 81.43603 at 30iterations 1.997560 45.63868 at 40iterations 1.170849 22.99611 at 50iterations 0.6849102 14.82637 at 60iterations 0.4003237 7.971138 at 70iterations 0.2334682 4.774692 at 80iterations 0.1358742 2.893402 at 90iterations 7.9039291E-02 1.580653 at 100iterations 4.5902468E-02 0.9626846 at 110iterations 2.6710555E-02 0.4838562 at 120iterations 1.5587036E-02 0.3453827 at 130iterations 9.1240741E-03 0.1747818 at 140iterations 5.3880587E-03 0.1223755 at 150iterations 3.2656807E-03 6.6680908E-02 at 160iterations 2.0419441E-03 4.7019958E-02 at 170iterations 1.3546984E-03 3.2592773E-02 at 180iterations finished qdiffx linear iterations at : 11:35:06 total time elapsed so far: 20.98000 # loops : 180 mean,max change (kT/e) : 1.3546984E-03 3.2592773E-02 energy calculations done at 20.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.14000 DelPhi exited at 11:35:06 21.144u 0.563s 0:22.01 98.5% 0+0k 0+0io 0pf+0w