Sat Oct 15 12:54:19 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 12:54:19 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2798 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: 0.5774721 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): -42.56600 19.08200 ymin,ymax (A): 5.339000 57.71100 zmin,zma (A): -20.13700 32.59600 x,y,z range (A): 61.64800 52.37200 52.73300 scale (grids/A): 0.5774721 object centre (A): -11.74200 31.52500 6.229500 number of atom coordinates read : 2798 total number of charged atoms : 2710 net assigned charge : 8.500011 assigned positive charge : 415.4071 centred at (gu) : 90.34951 89.37267 89.83923 assigned negative charge : -406.9088 centred at (gu) : 90.28184 89.34400 89.87279 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6829 nv = 96 ne = 84 npr = 50097 no. pairs analyzed = 50097 no. exposed pairs = 4396 no. arc points = 30712 no. surface atoms = 1445 nbur = 1353 mkacc time = 9.0000004E-02 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 = 1.512000 m= 364 mr = 3202 m= 0 mr = 39 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3952 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3080 ## 305 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8385 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4055482E-09 1.0368268E-09 midg,1,midg; midg,igrid,midg 1.3405018E-09 1.9290776E-09 1,midg,midg; igrid,midg,midg 4.0593728E-10 3.1921827E-09 gauss-seidel spectral radius is 0.9845365 estimated iterations to convergence 66 setup time was (sec) 0.3900000 now iterating at: 12:54:20 rms-change max change #iterations 9.0775780E-02 14.61403 at 10iterations 6.7717778E-03 0.9888363 at 20iterations 6.2740478E-04 0.1040421 at 30iterations 1.1680380E-04 1.4272928E-02 at 40iterations 3.5383113E-05 4.3819696E-03 at 50iterations finished qdiffx linear iterations at : 12:54:23 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 3.5383113E-05 4.3819696E-03 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 12:54:23 3.503u 0.199s 0:04.05 91.1% 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 12:54:23 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2798 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: 1.732416 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): -42.56600 19.08200 ymin,ymax (A): 5.339000 57.71100 zmin,zma (A): -20.13700 32.59600 x,y,z range (A): 61.64800 52.37200 52.73300 scale (grids/A): 1.732416 object centre (A): -11.74200 31.52500 6.229500 number of atom coordinates read : 2798 total number of charged atoms : 2710 net assigned charge : 8.500011 assigned positive charge : 415.4071 centred at (gu) : 91.04774 88.11715 89.51663 assigned negative charge : -406.9088 centred at (gu) : 90.84541 88.03173 89.61833 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 74058 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30712 grid for indexing accessible points = 1.400000 m= 26034 mr = 47889 m= 3919 mr = 17573 m= 175 mr = 2137 m= 2 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 36543 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 254 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 21102 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) : 0.5774721 object centre at (A) : -11.74200 31.52500 6.229500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.8314478E-03 -2.6438036E-03 midg,1,midg; midg,igrid,midg 2.2202123E-02 1.3438559E-02 1,midg,midg; igrid,midg,midg 1.2229836E-02 6.0183308E-03 gauss-seidel spectral radius is 0.9984249 estimated iterations to convergence 200 setup time was (sec) 0.5800000 now iterating at: 12:54:24 rms-change max change #iterations 3.637973 169.0322 at 10iterations 1.604490 58.55934 at 20iterations 0.7067268 25.72117 at 30iterations 0.3125472 11.28874 at 40iterations 0.1380968 4.999174 at 50iterations 6.0931578E-02 2.124266 at 60iterations 2.7037593E-02 0.9847403 at 70iterations 1.1950200E-02 0.4352951 at 80iterations 5.3117718E-03 0.1795769 at 90iterations 2.3718914E-03 8.0596924E-02 at 100iterations 1.0647997E-03 3.5702646E-02 at 110iterations 4.8310924E-04 1.5742302E-02 at 120iterations finished qdiffx linear iterations at : 12:54:31 total time elapsed so far: 7.870000 # loops : 120 mean,max change (kT/e) : 4.8310924E-04 1.5742302E-02 energy calculations done at 7.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.990000 DelPhi exited at 12:54:32 7.997u 0.239s 0:08.67 94.8% 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 Sat Oct 15 2011 at 12:54:32 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2798 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: 2.598624 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): -42.56600 19.08200 ymin,ymax (A): 5.339000 57.71100 zmin,zma (A): -20.13700 32.59600 x,y,z range (A): 61.64800 52.37200 52.73300 scale (grids/A): 2.598624 object centre (A): -11.74200 31.52500 6.229500 number of atom coordinates read : 2798 total number of charged atoms : 2710 net assigned charge : 8.500011 assigned positive charge : 415.4071 centred at (gu) : 91.57127 87.17539 89.27486 assigned negative charge : -406.9088 centred at (gu) : 91.26805 87.04776 89.42734 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 171399 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30712 grid for indexing accessible points = 1.400000 m= 84198 mr = 118145 m= 29860 mr = 64685 m= 6591 mr = 22484 m= 782 mr = 4653 m= 29 mr = 399 m= 0 mr = 8 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9300000 number of dielectric boundary points 82485 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 21669 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) : 1.732416 object centre at (A) : -11.74200 31.52500 6.229500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1004102 -3.0561887E-02 midg,1,midg; midg,igrid,midg 0.3329822 0.1558538 1,midg,midg; igrid,midg,midg 0.2290410 1.8341111E-02 gauss-seidel spectral radius is 0.9992321 estimated iterations to convergence 285 setup time was (sec) 1.160000 now iterating at: 12:54:33 rms-change max change #iterations 9.330029 314.9675 at 10iterations 5.561332 153.2831 at 20iterations 3.268693 77.03367 at 30iterations 1.910353 44.62958 at 40iterations 1.112092 24.85364 at 50iterations 0.6438490 15.48659 at 60iterations 0.3715847 8.191399 at 70iterations 0.2137088 4.377956 at 80iterations 0.1227367 2.628939 at 90iterations 7.0172913E-02 1.407324 at 100iterations 4.0131126E-02 0.8962345 at 110iterations 2.3036065E-02 0.4508514 at 120iterations 1.3135524E-02 0.2593613 at 130iterations 7.4825594E-03 0.1677608 at 140iterations 4.2740167E-03 9.3291283E-02 at 150iterations 2.4348807E-03 4.5921326E-02 at 160iterations 1.3885659E-03 2.9648781E-02 at 170iterations 7.9419377E-04 1.6664505E-02 at 180iterations finished qdiffx linear iterations at : 12:54:45 total time elapsed so far: 12.91000 # loops : 180 mean,max change (kT/e) : 7.9419377E-04 1.6664505E-02 energy calculations done at 12.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.04000 DelPhi exited at 12:54:46 13.040u 0.233s 0:13.61 97.5% 0+0k 0+0io 0pf+0w