Sun Oct 9 07:34:06 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+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 Sun Oct 9 2011 at 07:34:06 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1649 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7654103 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): -14.21700 26.41000 ymin,ymax (A): 3.756000 46.53500 zmin,zma (A): -1.407000 45.10400 x,y,z range (A): 40.62700 42.77900 46.51100 scale (grids/A): 0.7654103 object centre (A): 6.096500 25.14550 21.84850 number of atom coordinates read : 1649 total number of charged atoms : 1512 net assigned charge : -9.499993 assigned positive charge : 240.0202 centred at (gu) : 89.89919 89.79243 89.71403 assigned negative charge : -249.5201 centred at (gu) : 90.18182 89.99310 90.02825 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6547 nv = 96 ne = 84 npr = 35151 no. pairs analyzed = 35151 no. exposed pairs = 2111 no. arc points = 14944 no. surface atoms = 719 nbur = 930 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 507 mr = 3630 m= 2 mr = 118 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 102 time to turn everything in is 0.2300000 number of dielectric boundary points 3308 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1104 ## 77 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 6700 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2032542E-07 -6.7348418E-07 midg,1,midg; midg,igrid,midg -2.8842795E-08 -5.3321889E-07 1,midg,midg; igrid,midg,midg 7.5781799E-08 -6.5361979E-07 gauss-seidel spectral radius is 0.9910530 estimated iterations to convergence 86 setup time was (sec) 0.4800000 now iterating at: 07:34:06 rms-change max change #iterations 0.2436983 34.78453 at 10iterations 3.4575365E-02 4.590672 at 20iterations 4.9796877E-03 0.7122087 at 30iterations 7.1605999E-04 0.1009941 at 40iterations 1.0113282E-04 1.3750076E-02 at 50iterations finished qdiffx linear iterations at : 07:34:09 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 1.0113282E-04 1.3750076E-02 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 07:34:10 3.418u 0.200s 0:04.03 89.5% 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 07:34:10 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1649 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: 2.296231 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): -14.21700 26.41000 ymin,ymax (A): 3.756000 46.53500 zmin,zma (A): -1.407000 45.10400 x,y,z range (A): 40.62700 42.77900 46.51100 scale (grids/A): 2.296231 object centre (A): 6.096500 25.14550 21.84850 number of atom coordinates read : 1649 total number of charged atoms : 1512 net assigned charge : -9.499993 assigned positive charge : 240.0202 centred at (gu) : 89.69784 89.37749 89.14234 assigned negative charge : -249.5201 centred at (gu) : 90.54543 89.97933 90.08474 start vw surface at 0.1200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 68393 reading accessible surface arcs data from file ARCDAT no. of arc points read = 14944 grid for indexing accessible points = 1.400000 m= 28358 mr = 46626 m= 6505 mr = 21930 m= 682 mr = 4604 m= 28 mr = 384 m= 0 mr = 2 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 2436 time to turn everything in is 0.5400000 number of dielectric boundary points 30420 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 26 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 12061 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) : 0.7654103 object centre at (A) : 6.096500 25.14550 21.84850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.8975434E-02 -0.1911851 midg,1,midg; midg,igrid,midg -2.9126452E-02 -9.9581704E-02 1,midg,midg; igrid,midg,midg 5.3488757E-02 -6.8851195E-02 gauss-seidel spectral radius is 0.9989429 estimated iterations to convergence 243 setup time was (sec) 0.8400000 now iterating at: 07:34:11 rms-change max change #iterations 4.665213 270.6597 at 10iterations 2.386951 84.07005 at 20iterations 1.215151 41.91911 at 30iterations 0.6245481 19.72963 at 40iterations 0.3193982 9.382462 at 50iterations 0.1641899 5.149261 at 60iterations 8.4029928E-02 2.472302 at 70iterations 4.3052647E-02 1.396702 at 80iterations 2.2072991E-02 0.6509237 at 90iterations 1.1306458E-02 0.3471298 at 100iterations 5.7955594E-03 0.1695938 at 110iterations 2.9666915E-03 8.8989258E-02 at 120iterations finished qdiffx linear iterations at : 07:34:18 total time elapsed so far: 7.650000 # loops : 120 mean,max change (kT/e) : 2.9666915E-03 8.8989258E-02 energy calculations done at 7.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.830000 DelPhi exited at 07:34:18 7.833u 0.262s 0:08.47 95.5% 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 07:34:18 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 = 1649 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.444346 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): -14.21700 26.41000 ymin,ymax (A): 3.756000 46.53500 zmin,zma (A): -1.407000 45.10400 x,y,z range (A): 40.62700 42.77900 46.51100 scale (grids/A): 3.444346 object centre (A): 6.096500 25.14550 21.84850 number of atom coordinates read : 1649 total number of charged atoms : 1512 net assigned charge : -9.499993 assigned positive charge : 240.0202 centred at (gu) : 89.54679 89.06630 88.71359 assigned negative charge : -249.5201 centred at (gu) : 90.81815 89.96903 90.12711 start vw surface at 0.1200000 fill in re-entrant regions at 0.7700000 boundary points on vw surface= 157072 reading accessible surface arcs data from file ARCDAT no. of arc points read = 14944 grid for indexing accessible points = 1.400000 m= 85019 mr = 112099 m= 38690 mr = 70906 m= 12636 mr = 32535 m= 2783 mr = 10201 m= 362 mr = 2065 m= 20 mr = 235 m= 0 mr = 4 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 8144 time to turn everything in is 1.700000 number of dielectric boundary points 68537 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.840000 number of grid points assigned charge 12096 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) : 2.296231 object centre at (A) : 6.096500 25.14550 21.84850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1942306 -1.781765 midg,1,midg; midg,igrid,midg -0.2884516 -0.7476202 1,midg,midg; igrid,midg,midg 0.6031902 -0.3929791 gauss-seidel spectral radius is 0.9993185 estimated iterations to convergence 302 setup time was (sec) 2.020000 now iterating at: 07:34:21 rms-change max change #iterations 9.885509 278.6108 at 10iterations 5.794647 108.8100 at 20iterations 3.404433 65.93529 at 30iterations 2.003194 35.47326 at 40iterations 1.173904 20.00412 at 50iterations 0.6873579 12.99867 at 60iterations 0.4030421 7.545311 at 70iterations 0.2371681 4.298335 at 80iterations 0.1391450 2.631994 at 90iterations 8.1445336E-02 1.385450 at 100iterations 4.7835648E-02 0.7968102 at 110iterations 2.8066490E-02 0.5086975 at 120iterations 1.6469849E-02 0.2796974 at 130iterations 9.6494891E-03 0.1816006 at 140iterations 5.6717251E-03 9.0240479E-02 at 150iterations 3.3307818E-03 5.8706284E-02 at 160iterations 1.9544750E-03 3.4129143E-02 at 170iterations 1.1516133E-03 2.0110607E-02 at 180iterations finished qdiffx linear iterations at : 07:34:32 total time elapsed so far: 13.03000 # loops : 180 mean,max change (kT/e) : 1.1516133E-03 2.0110607E-02 energy calculations done at 13.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.20000 DelPhi exited at 07:34:32 13.205u 0.260s 0:13.77 97.7% 0+0k 0+0io 0pf+0w