Tue Oct 11 07:51:13 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 Tue Oct 11 2011 at 07:51:13 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2733 !!! WARNING: SEP 206 has a net charge of -0.4750 !!! WARNING: SEP 211 has a net charge of -0.4750 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: 0.6416727 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): -13.17900 42.30100 ymin,ymax (A): -22.36500 25.33300 zmin,zma (A): -5.379000 40.33800 x,y,z range (A): 55.48000 47.69800 45.71700 scale (grids/A): 0.6416727 object centre (A): 14.56100 1.484000 17.47950 number of atom coordinates read : 2733 total number of charged atoms : 2368 net assigned charge : 7.550014 assigned positive charge : 381.0852 centred at (gu) : 89.92501 88.80513 89.14234 assigned negative charge : -373.5357 centred at (gu) : 89.93679 88.76891 89.30608 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6775 nv = 96 ne = 84 npr = 51214 no. pairs analyzed = 51214 no. exposed pairs = 2922 no. arc points = 20393 no. surface atoms = 1004 nbur = 1729 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 346 mr = 3863 m= 2 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3225 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2025 ## 210 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8141 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.6369844E-08 -6.6723489E-09 midg,1,midg; midg,igrid,midg 9.0557046E-09 1.2195597E-08 1,midg,midg; igrid,midg,midg 1.2976713E-08 9.8611377E-09 gauss-seidel spectral radius is 0.9874011 estimated iterations to convergence 73 setup time was (sec) 0.5200000 now iterating at: 07:51:14 rms-change max change #iterations 0.1464928 21.43091 at 10iterations 1.5791913E-02 2.207947 at 20iterations 2.1155491E-03 0.3621826 at 30iterations 3.6550310E-04 5.5397034E-02 at 40iterations 7.5619610E-05 1.1405945E-02 at 50iterations finished qdiffx linear iterations at : 07:51:16 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 7.5619610E-05 1.1405945E-02 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 07:51:17 3.379u 0.144s 0:04.10 85.6% 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 Tue Oct 11 2011 at 07:51:17 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2733 !!! WARNING: SEP 206 has a net charge of -0.4750 !!! WARNING: SEP 211 has a net charge of -0.4750 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: 1.925018 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): -13.17900 42.30100 ymin,ymax (A): -22.36500 25.33300 zmin,zma (A): -5.379000 40.33800 x,y,z range (A): 55.48000 47.69800 45.71700 scale (grids/A): 1.925018 object centre (A): 14.56100 1.484000 17.47950 number of atom coordinates read : 2733 total number of charged atoms : 2368 net assigned charge : 7.550014 assigned positive charge : 381.0852 centred at (gu) : 89.77464 86.41496 87.42656 assigned negative charge : -373.5357 centred at (gu) : 89.81045 86.30666 87.91827 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 73099 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20393 grid for indexing accessible points = 1.400000 m= 26525 mr = 51939 m= 3844 mr = 19883 m= 210 mr = 2303 m= 6 mr = 83 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 0.5100000 number of dielectric boundary points 29476 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 146 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 18594 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) : 0.6416727 object centre at (A) : 14.56100 1.484000 17.47950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2326320E-02 -5.3046793E-03 midg,1,midg; midg,igrid,midg 6.0993168E-03 1.9996142E-02 1,midg,midg; igrid,midg,midg 1.9228769E-02 3.5947613E-02 gauss-seidel spectral radius is 0.9986465 estimated iterations to convergence 215 setup time was (sec) 0.7700000 now iterating at: 07:51:18 rms-change max change #iterations 4.245545 182.8933 at 10iterations 2.001661 71.53120 at 20iterations 0.9386327 35.20718 at 30iterations 0.4449603 13.64565 at 40iterations 0.2106694 6.630207 at 50iterations 9.8976977E-02 3.240444 at 60iterations 4.7051340E-02 1.608612 at 70iterations 2.2343684E-02 0.7665434 at 80iterations 1.0647247E-02 0.3230362 at 90iterations 5.1336577E-03 0.1580791 at 100iterations 2.5019431E-03 7.5607300E-02 at 110iterations 1.2458056E-03 4.5845032E-02 at 120iterations finished qdiffx linear iterations at : 07:51:25 total time elapsed so far: 7.420000 # loops : 120 mean,max change (kT/e) : 1.2458056E-03 4.5845032E-02 energy calculations done at 7.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.620000 DelPhi exited at 07:51:25 7.620u 0.168s 0:08.15 95.4% 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 Tue Oct 11 2011 at 07:51:26 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2733 !!! WARNING: SEP 206 has a net charge of -0.4750 !!! WARNING: SEP 211 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.887527 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): -13.17900 42.30100 ymin,ymax (A): -22.36500 25.33300 zmin,zma (A): -5.379000 40.33800 x,y,z range (A): 55.48000 47.69800 45.71700 scale (grids/A): 2.887527 object centre (A): 14.56100 1.484000 17.47950 number of atom coordinates read : 2733 total number of charged atoms : 2368 net assigned charge : 7.550014 assigned positive charge : 381.0852 centred at (gu) : 89.66187 84.62244 86.13972 assigned negative charge : -373.5357 centred at (gu) : 89.71562 84.46000 86.87740 start vw surface at 0.2400000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 168884 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20393 grid for indexing accessible points = 1.400000 m= 86364 mr = 124949 m= 30407 mr = 71893 m= 6795 mr = 24473 m= 967 mr = 5029 m= 55 mr = 661 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.8099999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.440000 number of dielectric boundary points 66444 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.580000 number of grid points assigned charge 18938 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) : 1.925018 object centre at (A) : 14.56100 1.484000 17.47950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3906215 -0.1156794 midg,1,midg; midg,igrid,midg 5.0477065E-02 0.2152197 1,midg,midg; igrid,midg,midg 7.3918864E-02 0.2771270 gauss-seidel spectral radius is 0.9992494 estimated iterations to convergence 288 setup time was (sec) 1.750000 now iterating at: 07:51:27 rms-change max change #iterations 9.747703 332.0811 at 10iterations 5.632855 116.9447 at 20iterations 3.249098 63.61213 at 30iterations 1.870162 39.35637 at 40iterations 1.072390 22.12254 at 50iterations 0.6173261 12.64407 at 60iterations 0.3541363 6.276472 at 70iterations 0.2028326 3.509132 at 80iterations 0.1163682 2.224966 at 90iterations 6.6779196E-02 1.352711 at 100iterations 3.8336072E-02 0.7303600 at 110iterations 2.2118494E-02 0.4167595 at 120iterations 1.2807956E-02 0.2340860 at 130iterations 7.4868221E-03 0.1600647 at 140iterations 4.4420282E-03 8.1176758E-02 at 150iterations 2.7053019E-03 5.3207397E-02 at 160iterations 1.7002964E-03 3.4969330E-02 at 170iterations 1.1136429E-03 2.0999908E-02 at 180iterations finished qdiffx linear iterations at : 07:51:38 total time elapsed so far: 12.75000 # loops : 180 mean,max change (kT/e) : 1.1136429E-03 2.0999908E-02 energy calculations done at 12.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.94000 DelPhi exited at 07:51:39 12.946u 0.203s 0:13.66 96.1% 0+0k 0+0io 0pf+0w