Sat Oct 8 11:40:52 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 8 2011 at 11:40:52 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 = 4432 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: 0.5675025 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): -27.53300 35.19800 ymin,ymax (A): 37.87700 95.89000 zmin,zma (A): 31.22600 89.84400 x,y,z range (A): 62.73100 58.01300 58.61800 scale (grids/A): 0.5675025 object centre (A): 3.832500 66.88350 60.53500 number of atom coordinates read : 4432 total number of charged atoms : 4272 net assigned charge : -4.999941 assigned positive charge : 663.8412 centred at (gu) : 90.85125 88.51576 88.92159 assigned negative charge : -668.8442 centred at (gu) : 90.74117 88.61401 89.06120 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 9128 nv = 96 ne = 84 npr = 93199 no. pairs analyzed = 93199 no. exposed pairs = 5003 no. arc points = 33786 no. surface atoms = 1714 nbur = 2718 mkacc time = 0.1500000 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= 426 mr = 5288 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 72 time to turn everything in is 0.3100000 number of dielectric boundary points 4237 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3623 ## 428 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 12063 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8483229E-09 -2.9786742E-09 midg,1,midg; midg,igrid,midg 1.9035560E-09 -2.0617481E-09 1,midg,midg; igrid,midg,midg -2.6091829E-09 1.9292627E-09 gauss-seidel spectral radius is 0.9840827 estimated iterations to convergence 65 setup time was (sec) 0.5200000 now iterating at: 11:40:53 rms-change max change #iterations 0.1083792 14.47537 at 10iterations 8.5652741E-03 1.157795 at 20iterations 1.0360497E-03 0.1350174 at 30iterations 2.8361051E-04 3.6019325E-02 at 40iterations 1.0613480E-04 1.3874054E-02 at 50iterations finished qdiffx linear iterations at : 11:40:56 total time elapsed so far: 3.570000 # loops : 50 mean,max change (kT/e) : 1.0613480E-04 1.3874054E-02 energy calculations done at 3.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.710000 DelPhi exited at 11:40:56 3.710u 0.190s 0:04.18 93.3% 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 8 2011 at 11:40:57 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4432 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: 1.702507 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): -27.53300 35.19800 ymin,ymax (A): 37.87700 95.89000 zmin,zma (A): 31.22600 89.84400 x,y,z range (A): 62.73100 58.01300 58.61800 scale (grids/A): 1.702507 object centre (A): 3.832500 66.88350 60.53500 number of atom coordinates read : 4432 total number of charged atoms : 4272 net assigned charge : -4.999941 assigned positive charge : 663.8412 centred at (gu) : 92.55231 85.54578 86.76343 assigned negative charge : -668.8442 centred at (gu) : 92.22297 85.84145 87.18286 start vw surface at 0.1200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 101810 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33786 grid for indexing accessible points = 1.400000 m= 35786 mr = 73858 m= 4418 mr = 26308 m= 141 mr = 2540 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 3747 time to turn everything in is 0.4900000 number of dielectric boundary points 39427 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 361 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 32978 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) : 0.5675025 object centre at (A) : 3.832500 66.88350 60.53500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7608536E-02 -2.7105264E-02 midg,1,midg; midg,igrid,midg 2.8430402E-02 -1.4293968E-02 1,midg,midg; igrid,midg,midg -2.8412538E-02 3.0337246E-02 gauss-seidel spectral radius is 0.9984614 estimated iterations to convergence 202 setup time was (sec) 0.7200000 now iterating at: 11:40:57 rms-change max change #iterations 4.598860 177.6291 at 10iterations 2.044577 58.45579 at 20iterations 0.9184372 31.19606 at 30iterations 0.4110462 11.59123 at 40iterations 0.1839290 5.529495 at 50iterations 8.2702532E-02 2.212482 at 60iterations 3.7068632E-02 1.171201 at 70iterations 1.6659416E-02 0.4716227 at 80iterations 7.5288480E-03 0.2420044 at 90iterations 3.4374429E-03 9.9899292E-02 at 100iterations 1.6061085E-03 4.9621582E-02 at 110iterations 7.7944872E-04 2.1839142E-02 at 120iterations finished qdiffx linear iterations at : 11:41:05 total time elapsed so far: 8.320000 # loops : 120 mean,max change (kT/e) : 7.7944872E-04 2.1839142E-02 energy calculations done at 8.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.470000 DelPhi exited at 11:41:06 8.472u 0.244s 0:08.97 97.1% 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 8 2011 at 11:41:06 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 = 4432 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: 2.553761 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): -27.53300 35.19800 ymin,ymax (A): 37.87700 95.89000 zmin,zma (A): 31.22600 89.84400 x,y,z range (A): 62.73100 58.01300 58.61800 scale (grids/A): 2.553761 object centre (A): 3.832500 66.88350 60.53500 number of atom coordinates read : 4432 total number of charged atoms : 4272 net assigned charge : -4.999941 assigned positive charge : 663.8412 centred at (gu) : 93.82813 83.31802 85.14474 assigned negative charge : -668.8442 centred at (gu) : 93.33427 83.76206 85.77425 start vw surface at 0.1200000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 236536 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33786 grid for indexing accessible points = 1.400000 m= 119719 mr = 179213 m= 38633 mr = 98690 m= 7456 mr = 30490 m= 655 mr = 5353 m= 8 mr = 359 m= 0 mr = 2 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 12667 time to turn everything in is 1.250000 number of dielectric boundary points 88900 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 34156 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) : 1.702507 object centre at (A) : 3.832500 66.88350 60.53500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5176328 -0.3360180 midg,1,midg; midg,igrid,midg 0.4196399 -0.2904808 1,midg,midg; igrid,midg,midg -0.3747980 0.2732277 gauss-seidel spectral radius is 0.9992396 estimated iterations to convergence 286 setup time was (sec) 1.520000 now iterating at: 11:41:07 rms-change max change #iterations 11.43493 391.7968 at 10iterations 6.671698 146.6407 at 20iterations 3.860513 89.03914 at 30iterations 2.236134 40.14138 at 40iterations 1.286591 23.39655 at 50iterations 0.7396145 13.81507 at 60iterations 0.4248796 6.952494 at 70iterations 0.2435237 4.223816 at 80iterations 0.1395472 2.247513 at 90iterations 7.9978004E-02 1.293114 at 100iterations 4.5692578E-02 0.7614131 at 110iterations 2.6137996E-02 0.4042778 at 120iterations 1.4961823E-02 0.2441400 at 130iterations 8.5725132E-03 0.1392918 at 140iterations 4.9302923E-03 8.7030411E-02 at 150iterations 2.8466941E-03 4.5963883E-02 at 160iterations 1.6635341E-03 2.7864456E-02 at 170iterations 9.8777912E-04 1.9613266E-02 at 180iterations finished qdiffx linear iterations at : 11:41:20 total time elapsed so far: 13.94000 # loops : 180 mean,max change (kT/e) : 9.8777912E-04 1.9613266E-02 energy calculations done at 13.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.07000 DelPhi exited at 11:41:20 14.070u 0.249s 0:14.59 98.0% 0+0k 0+0io 0pf+0w