Sat Oct 15 13:59:57 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+sph.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 = amb.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 13:59:57 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4430 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: ZN8 820 has a net charge of 1.4000 !!! WARNING: FE 3 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5144286 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): -16.60000 37.33000 ymin,ymax (A): -33.23100 31.38900 zmin,zma (A): -3.689000 65.51400 x,y,z range (A): 53.93000 64.62000 69.20300 scale (grids/A): 0.5144286 object centre (A): 10.36500 -0.9209995 30.91250 number of atom coordinates read : 4430 total number of charged atoms : 4186 net assigned charge : 3.700025 assigned positive charge : 660.0911 centred at (gu) : 90.25536 91.16325 87.55142 assigned negative charge : -656.3952 centred at (gu) : 90.10796 91.20004 87.57597 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7461 nv = 96 ne = 84 npr = 89890 no. pairs analyzed = 89890 no. exposed pairs = 5753 no. arc points = 39822 no. surface atoms = 1923 nbur = 2507 mkacc time = 0.2000000 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 = 1.652000 m= 319 mr = 3789 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 3989 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3836 ## 543 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 9882 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4472543E-10 -3.4048450E-12 midg,1,midg; midg,igrid,midg 1.1970576E-10 -5.9124962E-11 1,midg,midg; igrid,midg,midg -3.3373365E-10 4.9396470E-10 gauss-seidel spectral radius is 0.9806514 estimated iterations to convergence 59 setup time was (sec) 0.6300000 now iterating at: 13:59:58 rms-change max change #iterations 6.8537652E-02 11.11196 at 10iterations 4.1122935E-03 0.6679535 at 20iterations 5.8893306E-04 8.0812454E-02 at 30iterations 2.0838497E-04 2.5424659E-02 at 40iterations 7.9918900E-05 1.0754228E-02 at 50iterations finished qdiffx linear iterations at : 14:00:03 total time elapsed so far: 3.120000 # loops : 50 mean,max change (kT/e) : 7.9918900E-05 1.0754228E-02 energy calculations done at 3.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 14:00:06 3.299u 0.187s 0:08.98 38.6% 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 14:00:08 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4430 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: ZN8 820 has a net charge of 1.4000 !!! WARNING: FE 3 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.543286 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): -16.60000 37.33000 ymin,ymax (A): -33.23100 31.38900 zmin,zma (A): -3.689000 65.51400 x,y,z range (A): 53.93000 64.62000 69.20300 scale (grids/A): 1.543286 object centre (A): 10.36500 -0.9209995 30.91250 number of atom coordinates read : 4430 total number of charged atoms : 4186 net assigned charge : 3.700025 assigned positive charge : 660.0911 centred at (gu) : 90.76455 93.48856 82.65297 assigned negative charge : -656.3952 centred at (gu) : 90.32362 93.59966 82.72776 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 84275 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39822 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 24491 mr = 57336 m= 2263 mr = 15835 m= 54 mr = 867 m= 0 mr = 2 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 230 time to turn everything in is 0.5900000 number of dielectric boundary points 37043 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 502 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 31547 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) : 0.5144286 object centre at (A) : 10.36500 -0.9209995 30.91250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.6035638E-03 8.8520963E-03 midg,1,midg; midg,igrid,midg 1.6830112E-03 -1.3131849E-02 1,midg,midg; igrid,midg,midg -5.3461790E-03 9.7606163E-03 gauss-seidel spectral radius is 0.9981118 estimated iterations to convergence 183 setup time was (sec) 0.9200000 now iterating at: 14:00:11 rms-change max change #iterations 3.665408 147.3359 at 10iterations 1.497687 50.51273 at 20iterations 0.6126882 21.94986 at 30iterations 0.2506732 7.999165 at 40iterations 0.1033006 3.352688 at 50iterations 4.2238116E-02 1.387977 at 60iterations 1.7356809E-02 0.5840826 at 70iterations 7.1715391E-03 0.2639084 at 80iterations 2.9847273E-03 9.5972061E-02 at 90iterations 1.2725976E-03 4.4261932E-02 at 100iterations 5.7159824E-04 1.8857956E-02 at 110iterations 2.8592447E-04 9.1767311E-03 at 120iterations finished qdiffx linear iterations at : 14:00:29 total time elapsed so far: 7.960000 # loops : 120 mean,max change (kT/e) : 2.8592447E-04 9.1767311E-03 energy calculations done at 7.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.130000 DelPhi exited at 14:00:32 8.135u 0.229s 0:24.40 34.2% 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 14:00:33 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4430 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: ZN8 820 has a net charge of 1.4000 !!! WARNING: FE 3 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.314929 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): -16.60000 37.33000 ymin,ymax (A): -33.23100 31.38900 zmin,zma (A): -3.689000 65.51400 x,y,z range (A): 53.93000 64.62000 69.20300 scale (grids/A): 2.314929 object centre (A): 10.36500 -0.9209995 30.91250 number of atom coordinates read : 4430 total number of charged atoms : 4186 net assigned charge : 3.700025 assigned positive charge : 660.0911 centred at (gu) : 91.14646 95.23248 78.97927 assigned negative charge : -656.3952 centred at (gu) : 90.48532 95.39951 79.09157 start vw surface at 0.1500000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 196563 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39822 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 87603 mr = 141266 m= 21964 mr = 67460 m= 3119 mr = 15329 m= 142 mr = 1735 m= 1 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.8200001 no. cavity mid-points inaccessible to solvent = 852 time to turn everything in is 1.370000 number of dielectric boundary points 83555 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 57 iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 33396 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) : 1.543286 object centre at (A) : 10.36500 -0.9209995 30.91250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2013136 0.2488753 midg,1,midg; midg,igrid,midg 8.0970516E-03 -0.3553381 1,midg,midg; igrid,midg,midg -7.4418299E-02 0.1294168 gauss-seidel spectral radius is 0.9991559 estimated iterations to convergence 272 setup time was (sec) 1.670000 now iterating at: 14:00:40 rms-change max change #iterations 9.929139 287.3217 at 10iterations 5.674369 126.5962 at 20iterations 3.223341 70.60332 at 30iterations 1.821459 38.86295 at 40iterations 1.025176 21.76726 at 50iterations 0.5741585 13.42231 at 60iterations 0.3209653 6.977809 at 70iterations 0.1788715 3.834843 at 80iterations 9.9755980E-02 2.138645 at 90iterations 5.5551797E-02 1.215612 at 100iterations 3.0904111E-02 0.6360931 at 110iterations 1.7160144E-02 0.3653793 at 120iterations 9.5242104E-03 0.2007046 at 130iterations 5.2961740E-03 0.1047735 at 140iterations 2.9426306E-03 5.6551456E-02 at 150iterations 1.6364557E-03 3.4694672E-02 at 160iterations 9.1291044E-04 1.8363953E-02 at 170iterations 5.1339297E-04 9.9773407E-03 at 180iterations finished qdiffx linear iterations at : 14:01:07 total time elapsed so far: 11.50000 # loops : 180 mean,max change (kT/e) : 5.1339297E-04 9.9773407E-03 energy calculations done at 11.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.68000 DelPhi exited at 14:01:08 11.685u 0.165s 0:35.71 33.1% 0+0k 0+0io 0pf+0w