Sat Oct 8 13:58:06 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 Sat Oct 8 2011 at 13:58:06 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3043 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 0.6406795 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): -12.42800 43.13800 ymin,ymax (A): -22.36300 22.70000 zmin,zma (A): -7.076000 47.48300 x,y,z range (A): 55.56600 45.06300 54.55900 scale (grids/A): 0.6406795 object centre (A): 15.35500 0.1684990 20.20350 number of atom coordinates read : 3043 total number of charged atoms : 2896 net assigned charge : 1.4008060E-02 assigned positive charge : 457.8656 centred at (gu) : 88.74120 89.46723 91.50925 assigned negative charge : -457.8523 centred at (gu) : 88.74069 89.37829 91.41974 start vw surface at 0.1600000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8182 nv = 96 ne = 84 npr = 64274 no. pairs analyzed = 64274 no. exposed pairs = 3401 no. arc points = 23810 no. surface atoms = 1161 nbur = 1882 mkacc time = 0.2100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 399 mr = 4778 m= 2 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 3770 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2363 ## 195 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 10080 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.1807006E-09 1.7102970E-08 midg,1,midg; midg,igrid,midg -1.4206921E-08 1.0860309E-08 1,midg,midg; igrid,midg,midg -2.3181856E-10 -2.4936686E-11 gauss-seidel spectral radius is 0.9874080 estimated iterations to convergence 73 setup time was (sec) 0.7400000 now iterating at: 13:58:07 rms-change max change #iterations 0.1634651 24.45605 at 10iterations 1.6738271E-02 2.161896 at 20iterations 1.7511380E-03 0.2281666 at 30iterations 1.9721234E-04 2.4459839E-02 at 40iterations 2.6089816E-05 3.1318665E-03 at 50iterations finished qdiffx linear iterations at : 13:58:10 total time elapsed so far: 4.290000 # loops : 50 mean,max change (kT/e) : 2.6089816E-05 3.1318665E-03 energy calculations done at 4.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.500000 DelPhi exited at 13:58:11 4.503u 0.436s 0:05.25 93.9% 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 13:58:11 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3043 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 1.922039 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): -12.42800 43.13800 ymin,ymax (A): -22.36300 22.70000 zmin,zma (A): -7.076000 47.48300 x,y,z range (A): 55.56600 45.06300 54.55900 scale (grids/A): 1.922039 object centre (A): 15.35500 0.1684990 20.20350 number of atom coordinates read : 3043 total number of charged atoms : 2896 net assigned charge : 1.4008060E-02 assigned positive charge : 457.8656 centred at (gu) : 86.22347 88.40115 94.52697 assigned negative charge : -457.8523 centred at (gu) : 86.22176 88.13460 94.25890 start vw surface at 0.1700000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 89487 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23810 grid for indexing accessible points = 1.400000 m= 32352 mr = 64817 m= 4675 mr = 24323 m= 296 mr = 2809 m= 2 mr = 110 m= 0 mr = 0 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 234 time to turn everything in is 0.8800000 number of dielectric boundary points 34753 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 134 iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 22811 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) : 0.6406795 object centre at (A) : 15.35500 0.1684990 20.20350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8871082E-02 2.5404738E-02 midg,1,midg; midg,igrid,midg -9.5117866E-04 1.5840398E-02 1,midg,midg; igrid,midg,midg -3.7230544E-02 1.1293668E-02 gauss-seidel spectral radius is 0.9986908 estimated iterations to convergence 219 setup time was (sec) 1.210000 now iterating at: 13:58:13 rms-change max change #iterations 4.796710 200.5011 at 10iterations 2.288447 76.24612 at 20iterations 1.091142 32.02481 at 30iterations 0.5209512 16.08958 at 40iterations 0.2477201 7.180585 at 50iterations 0.1184067 3.293788 at 60iterations 5.6356829E-02 1.589187 at 70iterations 2.6952665E-02 0.7995253 at 80iterations 1.2833345E-02 0.3753605 at 90iterations 6.1091664E-03 0.1769638 at 100iterations 2.9192099E-03 8.6662292E-02 at 110iterations 1.3977099E-03 4.0386200E-02 at 120iterations finished qdiffx linear iterations at : 13:58:22 total time elapsed so far: 10.52000 # loops : 120 mean,max change (kT/e) : 1.3977099E-03 4.0386200E-02 energy calculations done at 10.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.73000 DelPhi exited at 13:58:22 10.738u 0.459s 0:11.49 97.3% 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 13:58:23 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3043 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 2.883058 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): -12.42800 43.13800 ymin,ymax (A): -22.36300 22.70000 zmin,zma (A): -7.076000 47.48300 x,y,z range (A): 55.56600 45.06300 54.55900 scale (grids/A): 2.883058 object centre (A): 15.35500 0.1684990 20.20350 number of atom coordinates read : 3043 total number of charged atoms : 2896 net assigned charge : 1.4008060E-02 assigned positive charge : 457.8656 centred at (gu) : 84.33519 87.60164 96.79032 assigned negative charge : -457.8523 centred at (gu) : 84.33267 87.20180 96.38826 start vw surface at 0.1600000 fill in re-entrant regions at 0.7700000 boundary points on vw surface= 207245 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23810 grid for indexing accessible points = 1.400000 m= 106267 mr = 156498 m= 36955 mr = 88610 m= 8420 mr = 29788 m= 1231 mr = 6134 m= 89 mr = 815 m= 0 mr = 27 time to grow re-entrant surface = 1.420000 no. cavity mid-points inaccessible to solvent = 718 time to turn everything in is 2.340000 number of dielectric boundary points 78335 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.490000 number of grid points assigned charge 23167 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) : 1.922039 object centre at (A) : 15.35500 0.1684990 20.20350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.6108359E-02 0.4811926 midg,1,midg; midg,igrid,midg 2.6346005E-03 0.1949906 1,midg,midg; igrid,midg,midg -0.6090927 0.2004651 gauss-seidel spectral radius is 0.9992765 estimated iterations to convergence 293 setup time was (sec) 2.710000 now iterating at: 13:58:26 rms-change max change #iterations 11.13126 349.1230 at 10iterations 6.567608 152.4582 at 20iterations 3.850584 90.89465 at 30iterations 2.249615 42.22655 at 40iterations 1.311609 22.51373 at 50iterations 0.7639971 12.55793 at 60iterations 0.4438016 8.231096 at 70iterations 0.2574624 4.623399 at 80iterations 0.1498267 2.559949 at 90iterations 8.6845189E-02 1.507481 at 100iterations 5.0393835E-02 0.8221121 at 110iterations 2.9199589E-02 0.4900970 at 120iterations 1.6917357E-02 0.2917647 at 130iterations 9.8404000E-03 0.1570654 at 140iterations 5.7063638E-03 9.4989777E-02 at 150iterations 3.3252691E-03 5.3970337E-02 at 160iterations 1.9394560E-03 3.2226563E-02 at 170iterations 1.1387615E-03 1.9414902E-02 at 180iterations finished qdiffx linear iterations at : 13:58:41 total time elapsed so far: 18.33000 # loops : 180 mean,max change (kT/e) : 1.1387615E-03 1.9414902E-02 energy calculations done at 18.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.54000 DelPhi exited at 13:58:42 18.548u 0.503s 0:19.34 98.4% 0+0k 0+0io 0pf+0w