Sun Oct 9 22:11:06 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 Sun Oct 9 2011 at 22:11:07 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3187 !!! WARNING: SEP 139 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5656540 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): -18.06800 37.91000 ymin,ymax (A): -4.408000 58.52800 zmin,zma (A): -5.052000 47.21500 x,y,z range (A): 55.97800 62.93600 52.26700 scale (grids/A): 0.5656540 object centre (A): 9.921000 27.06000 21.08150 number of atom coordinates read : 3187 total number of charged atoms : 3059 net assigned charge : 4.025008 assigned positive charge : 487.8008 centred at (gu) : 91.29918 88.67497 89.44427 assigned negative charge : -483.7771 centred at (gu) : 91.34335 88.58208 89.44367 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6671 nv = 96 ne = 84 npr = 61743 no. pairs analyzed = 61743 no. exposed pairs = 4243 no. arc points = 30745 no. surface atoms = 1418 nbur = 1769 mkacc time = 0.1100000 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= 289 mr = 3327 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 3629 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3015 ## 382 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 8620 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.2272310E-10 4.9606297E-10 midg,1,midg; midg,igrid,midg -1.1481199E-09 1.3856467E-09 1,midg,midg; igrid,midg,midg 8.8145635E-10 -1.4148095E-10 gauss-seidel spectral radius is 0.9838985 estimated iterations to convergence 65 setup time was (sec) 0.4300000 now iterating at: 22:11:07 rms-change max change #iterations 9.0304583E-02 13.55663 at 10iterations 6.4880601E-03 1.092105 at 20iterations 4.7918424E-04 7.5642586E-02 at 30iterations 3.6443529E-05 5.3040981E-03 at 40iterations 3.3743122E-06 4.5585632E-04 at 50iterations finished qdiffx linear iterations at : 22:11:10 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 3.3743122E-06 4.5585632E-04 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 22:11:10 3.482u 0.155s 0:03.93 92.3% 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 Sun Oct 9 2011 at 22:11:10 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3187 !!! WARNING: SEP 139 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.696962 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): -18.06800 37.91000 ymin,ymax (A): -4.408000 58.52800 zmin,zma (A): -5.052000 47.21500 x,y,z range (A): 55.97800 62.93600 52.26700 scale (grids/A): 1.696962 object centre (A): 9.921000 27.06000 21.08150 number of atom coordinates read : 3187 total number of charged atoms : 3059 net assigned charge : 4.025008 assigned positive charge : 487.8008 centred at (gu) : 93.89651 86.02408 88.33175 assigned negative charge : -483.7771 centred at (gu) : 94.02994 85.74612 88.33083 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 73152 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30745 grid for indexing accessible points = 1.400000 m= 22246 mr = 48211 m= 2526 mr = 14860 m= 114 mr = 1233 m= 6 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 177 time to turn everything in is 0.3600000 number of dielectric boundary points 33717 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 321 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 23580 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) : 0.5656540 object centre at (A) : 9.921000 27.06000 21.08150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5881608E-03 -2.9361196E-04 midg,1,midg; midg,igrid,midg -7.9126693E-03 -8.2501359E-03 1,midg,midg; igrid,midg,midg -1.7901086E-03 1.1523314E-02 gauss-seidel spectral radius is 0.9983574 estimated iterations to convergence 196 setup time was (sec) 0.5700000 now iterating at: 22:11:11 rms-change max change #iterations 3.777269 191.3156 at 10iterations 1.645829 66.32790 at 20iterations 0.7125856 24.84081 at 30iterations 0.3075982 12.49796 at 40iterations 0.1341273 4.490486 at 50iterations 5.8375314E-02 1.972220 at 60iterations 2.5310416E-02 0.8548889 at 70iterations 1.0983792E-02 0.4218025 at 80iterations 4.7937478E-03 0.1613731 at 90iterations 2.0820051E-03 7.3022842E-02 at 100iterations 9.0421701E-04 3.1135559E-02 at 110iterations 3.9455650E-04 1.2886047E-02 at 120iterations finished qdiffx linear iterations at : 22:11:18 total time elapsed so far: 7.730000 # loops : 120 mean,max change (kT/e) : 3.9455650E-04 1.2886047E-02 energy calculations done at 7.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.860000 DelPhi exited at 22:11:19 7.865u 0.205s 0:08.34 96.6% 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 Sun Oct 9 2011 at 22:11:19 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3187 !!! WARNING: SEP 139 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.545443 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): -18.06800 37.91000 ymin,ymax (A): -4.408000 58.52800 zmin,zma (A): -5.052000 47.21500 x,y,z range (A): 55.97800 62.93600 52.26700 scale (grids/A): 2.545443 object centre (A): 9.921000 27.06000 21.08150 number of atom coordinates read : 3187 total number of charged atoms : 3059 net assigned charge : 4.025008 assigned positive charge : 487.8008 centred at (gu) : 95.84461 84.03603 87.49744 assigned negative charge : -483.7771 centred at (gu) : 96.04494 83.61906 87.49617 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 170013 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30745 grid for indexing accessible points = 1.400000 m= 76319 mr = 118478 m= 22235 mr = 59127 m= 4000 mr = 16395 m= 411 mr = 2588 m= 24 mr = 219 m= 0 mr = 4 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 574 time to turn everything in is 0.8700000 number of dielectric boundary points 76191 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 24450 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) : 1.696962 object centre at (A) : 9.921000 27.06000 21.08150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.0107843E-02 -8.3779672E-04 midg,1,midg; midg,igrid,midg -0.2470057 -0.4798419 1,midg,midg; igrid,midg,midg -0.1225035 0.1807130 gauss-seidel spectral radius is 0.9992014 estimated iterations to convergence 279 setup time was (sec) 1.110000 now iterating at: 22:11:20 rms-change max change #iterations 9.689709 314.8480 at 10iterations 5.635447 195.4948 at 20iterations 3.241042 79.37831 at 30iterations 1.854466 47.83817 at 40iterations 1.062060 27.73453 at 50iterations 0.6038243 14.73224 at 60iterations 0.3421091 8.118973 at 70iterations 0.1941443 3.990955 at 80iterations 0.1096985 2.238297 at 90iterations 6.2025882E-02 1.369509 at 100iterations 3.4961443E-02 0.7084579 at 110iterations 1.9726358E-02 0.4008694 at 120iterations 1.1139200E-02 0.2170639 at 130iterations 6.2682186E-03 0.1249056 at 140iterations 3.5350339E-03 6.9213867E-02 at 150iterations 1.9895034E-03 4.0271759E-02 at 160iterations 1.1202341E-03 2.3498535E-02 at 170iterations 6.3059357E-04 1.1823654E-02 at 180iterations finished qdiffx linear iterations at : 22:11:32 total time elapsed so far: 12.71000 # loops : 180 mean,max change (kT/e) : 6.3059357E-04 1.1823654E-02 energy calculations done at 12.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.83000 DelPhi exited at 22:11:32 12.837u 0.217s 0:13.32 97.8% 0+0k 0+0io 0pf+0w