Sat Oct 8 13:55:11 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 13:55:11 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6407949 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): -12.40600 43.15000 ymin,ymax (A): -22.49700 22.40400 zmin,zma (A): -7.351000 47.19900 x,y,z range (A): 55.55600 44.90100 54.55000 scale (grids/A): 0.6407949 object centre (A): 15.37200 -4.6500206E-02 19.92400 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) : 88.77346 89.47532 91.69073 assigned negative charge : -457.8523 centred at (gu) : 88.77348 89.38406 91.59277 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8235 nv = 96 ne = 84 npr = 64021 no. pairs analyzed = 64021 no. exposed pairs = 3454 no. arc points = 24028 no. surface atoms = 1181 nbur = 1862 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 414 mr = 4799 m= 2 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3800 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2329 ## 208 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 10062 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.7239718E-09 1.9465283E-08 midg,1,midg; midg,igrid,midg -1.4640528E-08 1.1149585E-08 1,midg,midg; igrid,midg,midg -1.9548611E-10 -1.1748573E-10 gauss-seidel spectral radius is 0.9874137 estimated iterations to convergence 73 setup time was (sec) 0.6700000 now iterating at: 13:55:12 rms-change max change #iterations 0.1614962 24.02515 at 10iterations 1.6610917E-02 2.329967 at 20iterations 1.7140819E-03 0.2032623 at 30iterations 1.9854297E-04 2.6788712E-02 at 40iterations 2.6658974E-05 3.2043457E-03 at 50iterations finished qdiffx linear iterations at : 13:55:17 total time elapsed so far: 5.080000 # loops : 50 mean,max change (kT/e) : 2.6658974E-05 3.2043457E-03 energy calculations done at 5.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.260000 DelPhi exited at 13:55:17 5.266u 0.453s 0:06.03 94.6% 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 Sat Oct 8 2011 at 13:55:17 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: 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.922385 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): -12.40600 43.15000 ymin,ymax (A): -22.49700 22.40400 zmin,zma (A): -7.351000 47.19900 x,y,z range (A): 55.55600 44.90100 54.55000 scale (grids/A): 1.922385 object centre (A): 15.37200 -4.6500206E-02 19.92400 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) : 86.31996 88.42530 95.07178 assigned negative charge : -457.8523 centred at (gu) : 86.32030 88.15205 94.77834 start vw surface at 0.1400000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 89491 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24028 grid for indexing accessible points = 1.400000 m= 32506 mr = 64670 m= 4896 mr = 24473 m= 300 mr = 3027 m= 5 mr = 92 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 270 time to turn everything in is 0.7600000 number of dielectric boundary points 34937 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 169 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 22820 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) : 0.6407949 object centre at (A) : 15.37200 -4.6500206E-02 19.92400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0435192E-02 2.2091677E-02 midg,1,midg; midg,igrid,midg -2.7392157E-03 2.0655865E-02 1,midg,midg; igrid,midg,midg -3.4413233E-02 1.0225593E-02 gauss-seidel spectral radius is 0.9986927 estimated iterations to convergence 219 setup time was (sec) 1.110000 now iterating at: 13:55:19 rms-change max change #iterations 4.793302 167.0227 at 10iterations 2.291209 67.10962 at 20iterations 1.090652 34.23465 at 30iterations 0.5200510 15.83327 at 40iterations 0.2481084 7.176458 at 50iterations 0.1182989 3.481941 at 60iterations 5.6561403E-02 1.709509 at 70iterations 2.7020402E-02 0.7611504 at 80iterations 1.2832702E-02 0.3534203 at 90iterations 6.1493213E-03 0.1712399 at 100iterations 2.9369411E-03 8.4297180E-02 at 110iterations 1.4029042E-03 4.1191101E-02 at 120iterations finished qdiffx linear iterations at : 13:55:30 total time elapsed so far: 12.60000 # loops : 120 mean,max change (kT/e) : 1.4029042E-03 4.1191101E-02 energy calculations done at 12.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.78000 DelPhi exited at 13:55:31 12.787u 0.512s 0:13.60 97.7% 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 13:55:31 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.883577 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): -12.40600 43.15000 ymin,ymax (A): -22.49700 22.40400 zmin,zma (A): -7.351000 47.19900 x,y,z range (A): 55.55600 44.90100 54.55000 scale (grids/A): 2.883577 object centre (A): 15.37200 -4.6500206E-02 19.92400 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) : 84.47981 87.63789 97.60730 assigned negative charge : -457.8523 centred at (gu) : 84.48035 87.22808 97.16741 start vw surface at 0.1300000 fill in re-entrant regions at 0.6300000 boundary points on vw surface= 207482 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24028 grid for indexing accessible points = 1.400000 m= 106434 mr = 156241 m= 37596 mr = 88684 m= 8635 mr = 30458 m= 1221 mr = 6364 m= 64 mr = 777 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 1.190000 no. cavity mid-points inaccessible to solvent = 982 time to turn everything in is 1.950000 number of dielectric boundary points 78892 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.110000 number of grid points assigned charge 23168 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) : 1.922385 object centre at (A) : 15.37200 -4.6500206E-02 19.92400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1040229 0.3461816 midg,1,midg; midg,igrid,midg -1.8561589E-02 0.2490361 1,midg,midg; igrid,midg,midg -0.5849414 0.1547500 gauss-seidel spectral radius is 0.9992775 estimated iterations to convergence 294 setup time was (sec) 2.340000 now iterating at: 13:55:34 rms-change max change #iterations 11.07953 498.0964 at 10iterations 6.491118 130.8795 at 20iterations 3.792465 77.71725 at 30iterations 2.213505 45.88913 at 40iterations 1.285254 24.00702 at 50iterations 0.7477977 13.17281 at 60iterations 0.4344117 7.651843 at 70iterations 0.2518084 4.431423 at 80iterations 0.1461693 2.640326 at 90iterations 8.4662326E-02 1.488123 at 100iterations 4.9117263E-02 0.7908964 at 110iterations 2.8409775E-02 0.4619961 at 120iterations 1.6484616E-02 0.2655897 at 130iterations 9.5688738E-03 0.1588995 at 140iterations 5.5530299E-03 9.6027374E-02 at 150iterations 3.2292546E-03 5.5633545E-02 at 160iterations 1.8887303E-03 3.0151367E-02 at 170iterations 1.1085711E-03 1.8280029E-02 at 180iterations finished qdiffx linear iterations at : 13:55:53 total time elapsed so far: 21.54000 # loops : 180 mean,max change (kT/e) : 1.1085711E-03 1.8280029E-02 energy calculations done at 21.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.71000 DelPhi exited at 13:55:54 21.713u 0.580s 0:22.54 98.8% 0+0k 0+0io 0pf+0w