Wed Feb 15 08:55:58 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:55:58 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2466 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.6374674 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): -4.583000 45.91200 ymin,ymax (A): 10.52800 56.46000 zmin,zma (A): 9.758000 65.60400 x,y,z range (A): 50.49500 45.93200 55.84600 scale (grids/A): 0.6374674 object centre (A): 20.66450 33.49400 37.68100 number of atom coordinates read : 2466 total number of charged atoms : 2330 net assigned charge : 8.500018 assigned positive charge : 370.3150 centred at (gu) : 89.37457 90.98524 90.14650 assigned negative charge : -361.8158 centred at (gu) : 89.31995 90.90057 90.00490 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 6663 nv = 96 ne = 84 npr = 50543 no. pairs analyzed = 50543 no. exposed pairs = 3104 no. arc points = 21444 no. surface atoms = 1049 nbur = 1417 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 354 mr = 3580 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 3410 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2192 ## 227 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 8094 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.0357008E-09 2.6377235E-08 midg,1,midg; midg,igrid,midg 2.3372686E-09 2.4599590E-08 1,midg,midg; igrid,midg,midg 6.6220522E-09 1.4844888E-08 gauss-seidel spectral radius is 0.9872378 estimated iterations to convergence 72 setup time was (sec) 0.6300000 now iterating at: 08:55:59 rms-change max change #iterations 0.1374217 20.34312 at 10iterations 1.3322365E-02 1.831318 at 20iterations 1.2948777E-03 0.1811523 at 30iterations 1.3545585E-04 1.9006729E-02 at 40iterations 1.7819671E-05 2.5215149E-03 at 50iterations finished qdiffx linear iterations at : 08:56:02 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 1.7819671E-05 2.5215149E-03 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.610000 DelPhi exited at 08:56:03 3.618u 0.171s 0:04.68 80.7% 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 Wed Feb 15 2012 at 08:56:03 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2466 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.912402 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): -4.583000 45.91200 ymin,ymax (A): 10.52800 56.46000 zmin,zma (A): 9.758000 65.60400 x,y,z range (A): 50.49500 45.93200 55.84600 scale (grids/A): 1.912402 object centre (A): 20.66450 33.49400 37.68100 number of atom coordinates read : 2466 total number of charged atoms : 2330 net assigned charge : 8.500018 assigned positive charge : 370.3150 centred at (gu) : 88.12311 92.95525 90.43904 assigned negative charge : -361.8158 centred at (gu) : 87.95977 92.70158 90.01444 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 71878 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21444 grid for indexing accessible points = 1.400000 m= 25160 mr = 49402 m= 3496 mr = 17952 m= 179 mr = 1913 m= 3 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 357 time to turn everything in is 0.5700000 number of dielectric boundary points 31411 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 176 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 18310 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) : 0.6374674 object centre at (A) : 20.66450 33.49400 37.68100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2705695E-02 6.4851373E-02 midg,1,midg; midg,igrid,midg -1.6454974E-02 1.0392563E-02 1,midg,midg; igrid,midg,midg 2.9043758E-02 4.0590003E-02 gauss-seidel spectral radius is 0.9986353 estimated iterations to convergence 215 setup time was (sec) 0.8700000 now iterating at: 08:56:04 rms-change max change #iterations 4.104474 171.0509 at 10iterations 1.916702 71.73691 at 20iterations 0.8966101 29.37230 at 30iterations 0.4195342 15.05597 at 40iterations 0.1968184 6.707326 at 50iterations 9.1901638E-02 2.871468 at 60iterations 4.3148514E-02 1.601967 at 70iterations 2.0174269E-02 0.6325397 at 80iterations 9.4829611E-03 0.3118949 at 90iterations 4.4342135E-03 0.1592407 at 100iterations 2.0799432E-03 7.2048187E-02 at 110iterations 9.7575434E-04 2.8726578E-02 at 120iterations finished qdiffx linear iterations at : 08:56:11 total time elapsed so far: 7.490000 # loops : 120 mean,max change (kT/e) : 9.7575434E-04 2.8726578E-02 energy calculations done at 7.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.690000 DelPhi exited at 08:56:12 7.694u 0.298s 0:08.61 92.6% 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 Wed Feb 15 2012 at 08:56:12 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2466 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.868603 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): -4.583000 45.91200 ymin,ymax (A): 10.52800 56.46000 zmin,zma (A): 9.758000 65.60400 x,y,z range (A): 50.49500 45.93200 55.84600 scale (grids/A): 2.868603 object centre (A): 20.66450 33.49400 37.68100 number of atom coordinates read : 2466 total number of charged atoms : 2330 net assigned charge : 8.500018 assigned positive charge : 370.3150 centred at (gu) : 87.18443 94.43269 90.65846 assigned negative charge : -361.8158 centred at (gu) : 86.93966 94.05229 90.02170 start vw surface at 0.1700000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 166376 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21444 grid for indexing accessible points = 1.400000 m= 82354 mr = 120186 m= 28012 mr = 66364 m= 6022 mr = 21795 m= 719 mr = 4116 m= 39 mr = 358 m= 0 mr = 7 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 1182 time to turn everything in is 1.390000 number of dielectric boundary points 70696 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.530000 number of grid points assigned charge 18634 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) : 1.912402 object centre at (A) : 20.66450 33.49400 37.68100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0855691E-02 0.5888696 midg,1,midg; midg,igrid,midg -0.1454378 7.9284847E-02 1,midg,midg; igrid,midg,midg 0.2964217 0.4743636 gauss-seidel spectral radius is 0.9992569 estimated iterations to convergence 290 setup time was (sec) 1.720000 now iterating at: 08:56:14 rms-change max change #iterations 9.754894 513.4543 at 10iterations 5.724202 175.7200 at 20iterations 3.347592 65.73312 at 30iterations 1.949714 36.27125 at 40iterations 1.130183 20.64105 at 50iterations 0.6543967 12.18090 at 60iterations 0.3779691 7.636023 at 70iterations 0.2182353 3.899318 at 80iterations 0.1260461 2.241786 at 90iterations 7.2515629E-02 1.345779 at 100iterations 4.1819565E-02 0.8103924 at 110iterations 2.3999117E-02 0.4638786 at 120iterations 1.3819917E-02 0.2544723 at 130iterations 7.9167476E-03 0.1484795 at 140iterations 4.5458018E-03 8.2691193E-02 at 150iterations 2.6163133E-03 4.9170017E-02 at 160iterations 1.5053079E-03 2.5848389E-02 at 170iterations 8.6449768E-04 1.5983582E-02 at 180iterations finished qdiffx linear iterations at : 08:56:25 total time elapsed so far: 12.67000 # loops : 180 mean,max change (kT/e) : 8.6449768E-04 1.5983582E-02 energy calculations done at 12.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.87000 DelPhi exited at 08:56:26 12.872u 0.203s 0:13.69 95.4% 0+0k 0+0io 0pf+0w