Tue Oct 11 06:39:18 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 Tue Oct 11 2011 at 06:39:18 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 = 2053 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: 0.6853271 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): -20.64300 24.53600 ymin,ymax (A): -27.68200 12.14100 zmin,zma (A): -15.73200 36.21400 x,y,z range (A): 45.17900 39.82300 51.94600 scale (grids/A): 0.6853271 object centre (A): 1.946501 -7.770500 10.24100 number of atom coordinates read : 2053 total number of charged atoms : 1938 net assigned charge : 6.500009 assigned positive charge : 312.8170 centred at (gu) : 90.01990 90.69570 90.06673 assigned negative charge : -306.3172 centred at (gu) : 89.88470 90.67357 90.00949 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6502 nv = 96 ne = 84 npr = 41170 no. pairs analyzed = 41170 no. exposed pairs = 2458 no. arc points = 16975 no. surface atoms = 835 nbur = 1218 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 391 mr = 3698 m= 2 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3131 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1696 ## 183 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 7526 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4964025E-08 4.9195677E-08 midg,1,midg; midg,igrid,midg 2.2323468E-08 4.4011113E-08 1,midg,midg; igrid,midg,midg -8.0153519E-09 7.1135936E-08 gauss-seidel spectral radius is 0.9889056 estimated iterations to convergence 77 setup time was (sec) 0.4700000 now iterating at: 06:39:18 rms-change max change #iterations 0.1739043 24.80246 at 10iterations 1.9886658E-02 2.834852 at 20iterations 2.4128465E-03 0.3339157 at 30iterations 3.2316640E-04 5.0430298E-02 at 40iterations 5.9548915E-05 7.8887939E-03 at 50iterations finished qdiffx linear iterations at : 06:39:21 total time elapsed so far: 2.850000 # loops : 50 mean,max change (kT/e) : 5.9548915E-05 7.8887939E-03 energy calculations done at 2.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.020000 DelPhi exited at 06:39:21 3.027u 0.137s 0:03.66 86.0% 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 06:39:21 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 = 2053 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: 2.055981 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): -20.64300 24.53600 ymin,ymax (A): -27.68200 12.14100 zmin,zma (A): -15.73200 36.21400 x,y,z range (A): 45.17900 39.82300 51.94600 scale (grids/A): 2.055981 object centre (A): 1.946501 -7.770500 10.24100 number of atom coordinates read : 2053 total number of charged atoms : 1938 net assigned charge : 6.500009 assigned positive charge : 312.8170 centred at (gu) : 90.05965 92.08695 90.20016 assigned negative charge : -306.3172 centred at (gu) : 89.65424 92.02083 90.02865 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 69471 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16975 grid for indexing accessible points = 1.400000 m= 26777 mr = 49114 m= 4771 mr = 20220 m= 386 mr = 3053 m= 2 mr = 182 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 0.5000000 number of dielectric boundary points 28838 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 114 iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 15372 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) : 0.6853271 object centre at (A) : 1.946501 -7.770500 10.24100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.6648836E-02 4.6002891E-02 midg,1,midg; midg,igrid,midg 6.3103656E-03 2.7062224E-02 1,midg,midg; igrid,midg,midg 2.5505910E-03 2.5921442E-02 gauss-seidel spectral radius is 0.9987612 estimated iterations to convergence 225 setup time was (sec) 0.7600000 now iterating at: 06:39:22 rms-change max change #iterations 4.316991 178.8478 at 10iterations 2.086842 86.70186 at 20iterations 1.015186 32.54148 at 30iterations 0.4959634 16.18820 at 40iterations 0.2405736 8.699776 at 50iterations 0.1167076 3.587032 at 60iterations 5.6881558E-02 1.883978 at 70iterations 2.7703127E-02 0.8878593 at 80iterations 1.3465632E-02 0.4135590 at 90iterations 6.5594628E-03 0.1971893 at 100iterations 3.2149507E-03 0.1005325 at 110iterations 1.5846865E-03 4.9505234E-02 at 120iterations finished qdiffx linear iterations at : 06:39:28 total time elapsed so far: 6.680000 # loops : 120 mean,max change (kT/e) : 1.5846865E-03 4.9505234E-02 energy calculations done at 6.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.860000 DelPhi exited at 06:39:29 6.862u 0.164s 0:07.56 92.8% 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 06:39:29 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 = 2053 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: 3.083972 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): -20.64300 24.53600 ymin,ymax (A): -27.68200 12.14100 zmin,zma (A): -15.73200 36.21400 x,y,z range (A): 45.17900 39.82300 51.94600 scale (grids/A): 3.083972 object centre (A): 1.946501 -7.770500 10.24100 number of atom coordinates read : 2053 total number of charged atoms : 1938 net assigned charge : 6.500009 assigned positive charge : 312.8170 centred at (gu) : 90.08951 93.13036 90.30022 assigned negative charge : -306.3172 centred at (gu) : 89.48137 93.03116 90.04299 start vw surface at 0.1300000 fill in re-entrant regions at 0.6900000 boundary points on vw surface= 160280 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16975 grid for indexing accessible points = 1.400000 m= 84883 mr = 118562 m= 32988 mr = 70279 m= 8974 mr = 26960 m= 1548 mr = 6774 m= 161 mr = 1117 m= 4 mr = 97 m= 0 mr = 0 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.520000 number of dielectric boundary points 65049 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 15504 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) : 2.055981 object centre at (A) : 1.946501 -7.770500 10.24100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8389351 0.4334941 midg,1,midg; midg,igrid,midg 4.4971846E-02 0.2177374 1,midg,midg; igrid,midg,midg 8.5033596E-02 0.2119903 gauss-seidel spectral radius is 0.9992756 estimated iterations to convergence 293 setup time was (sec) 1.800000 now iterating at: 06:39:31 rms-change max change #iterations 9.734328 326.5287 at 10iterations 5.692974 123.9384 at 20iterations 3.336861 63.24813 at 30iterations 1.945162 41.37655 at 40iterations 1.137021 21.02225 at 50iterations 0.6621180 13.15661 at 60iterations 0.3845975 7.824255 at 70iterations 0.2238609 4.070507 at 80iterations 0.1299755 2.482630 at 90iterations 7.5593852E-02 1.500828 at 100iterations 4.3985374E-02 0.7553964 at 110iterations 2.5673414E-02 0.4664860 at 120iterations 1.4980715E-02 0.2735596 at 130iterations 8.8163661E-03 0.1656113 at 140iterations 5.2627604E-03 9.9596977E-02 at 150iterations 3.2102934E-03 5.9444427E-02 at 160iterations 2.0239330E-03 4.0380478E-02 at 170iterations 1.3390211E-03 2.4404526E-02 at 180iterations finished qdiffx linear iterations at : 06:39:40 total time elapsed so far: 11.34000 # loops : 180 mean,max change (kT/e) : 1.3390211E-03 2.4404526E-02 energy calculations done at 11.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.50000 DelPhi exited at 06:39:41 11.506u 0.192s 0:12.21 95.7% 0+0k 0+0io 0pf+0w