Sun Oct 9 02:51:56 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 02:51:56 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 = 2166 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6368401 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): -16.71700 23.66700 ymin,ymax (A): 0.8479999 44.04000 zmin,zma (A): -19.42800 36.47300 x,y,z range (A): 40.38400 43.19200 55.90100 scale (grids/A): 0.6368401 object centre (A): 3.475000 22.44400 8.522502 number of atom coordinates read : 2166 total number of charged atoms : 2034 net assigned charge : -3.999991 assigned positive charge : 322.4867 centred at (gu) : 90.51587 90.43813 90.62128 assigned negative charge : -326.4870 centred at (gu) : 90.51320 90.41731 90.62125 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5819 nv = 96 ne = 84 npr = 45754 no. pairs analyzed = 45754 no. exposed pairs = 2456 no. arc points = 17069 no. surface atoms = 843 nbur = 1323 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 318 mr = 3383 m= 1 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.1800000 number of dielectric boundary points 2706 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1656 ## 148 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 6939 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.6847974E-09 -6.0564473E-09 midg,1,midg; midg,igrid,midg -6.5687988E-09 -3.7740233E-09 1,midg,midg; igrid,midg,midg -4.9999738E-09 -5.6585465E-09 gauss-seidel spectral radius is 0.9871811 estimated iterations to convergence 72 setup time was (sec) 0.3600000 now iterating at: 02:51:57 rms-change max change #iterations 0.1293351 18.45037 at 10iterations 1.3655495E-02 2.208870 at 20iterations 2.3964599E-03 0.4530296 at 30iterations 7.0503866E-04 0.1464767 at 40iterations 2.3511873E-04 4.9148560E-02 at 50iterations finished qdiffx linear iterations at : 02:51:59 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 2.3511873E-04 4.9148560E-02 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 02:52:00 3.331u 0.172s 0:03.77 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 Sun Oct 9 2011 at 02:52:00 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 = 2166 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.910520 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): -16.71700 23.66700 ymin,ymax (A): 0.8479999 44.04000 zmin,zma (A): -19.42800 36.47300 x,y,z range (A): 40.38400 43.19200 55.90100 scale (grids/A): 1.910520 object centre (A): 3.475000 22.44400 8.522502 number of atom coordinates read : 2166 total number of charged atoms : 2034 net assigned charge : -3.999991 assigned positive charge : 322.4867 centred at (gu) : 91.54749 91.31425 91.86372 assigned negative charge : -326.4870 centred at (gu) : 91.53954 91.25204 91.86377 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 62910 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17069 grid for indexing accessible points = 1.400000 m= 22694 mr = 44802 m= 3623 mr = 17225 m= 221 mr = 2447 m= 4 mr = 94 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 572 time to turn everything in is 0.3000000 number of dielectric boundary points 24884 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 131 iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 15999 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) : 0.6368401 object centre at (A) : 3.475000 22.44400 8.522502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.0069499E-03 9.3942396E-03 midg,1,midg; midg,igrid,midg -4.0459996E-03 -1.1851999E-02 1,midg,midg; igrid,midg,midg -3.9568678E-03 -7.3873424E-03 gauss-seidel spectral radius is 0.9985887 estimated iterations to convergence 211 setup time was (sec) 0.5000000 now iterating at: 02:52:01 rms-change max change #iterations 3.854717 157.1290 at 10iterations 1.790608 61.53214 at 20iterations 0.8300188 29.48212 at 30iterations 0.3870661 13.79163 at 40iterations 0.1793249 6.100498 at 50iterations 8.3950587E-02 2.901716 at 60iterations 3.9218601E-02 1.472152 at 70iterations 1.8627297E-02 0.6173325 at 80iterations 9.0965256E-03 0.3708344 at 90iterations 4.6617752E-03 0.1881981 at 100iterations 2.5698107E-03 0.1082954 at 110iterations 1.5513058E-03 7.4684143E-02 at 120iterations finished qdiffx linear iterations at : 02:52:08 total time elapsed so far: 7.490000 # loops : 120 mean,max change (kT/e) : 1.5513058E-03 7.4684143E-02 energy calculations done at 7.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.630000 DelPhi exited at 02:52:08 7.631u 0.214s 0:08.12 96.5% 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 02:52:08 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 = 2166 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.865781 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): -16.71700 23.66700 ymin,ymax (A): 0.8479999 44.04000 zmin,zma (A): -19.42800 36.47300 x,y,z range (A): 40.38400 43.19200 55.90100 scale (grids/A): 2.865781 object centre (A): 3.475000 22.44400 8.522502 number of atom coordinates read : 2166 total number of charged atoms : 2034 net assigned charge : -3.999991 assigned positive charge : 322.4867 centred at (gu) : 92.32118 91.97124 92.79549 assigned negative charge : -326.4870 centred at (gu) : 92.30929 91.87804 92.79562 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 145653 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17069 grid for indexing accessible points = 1.400000 m= 73959 mr = 108406 m= 26976 mr = 61505 m= 6658 mr = 22230 m= 1045 mr = 5318 m= 65 mr = 777 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 2083 time to turn everything in is 0.7900000 number of dielectric boundary points 56097 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 16271 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) : 1.910520 object centre at (A) : 3.475000 22.44400 8.522502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4425080 0.2338472 midg,1,midg; midg,igrid,midg -4.7511108E-02 -0.1372373 1,midg,midg; igrid,midg,midg -6.2560484E-02 -5.4045621E-02 gauss-seidel spectral radius is 0.9992290 estimated iterations to convergence 284 setup time was (sec) 1.030000 now iterating at: 02:52:09 rms-change max change #iterations 8.959767 362.2008 at 10iterations 5.133662 128.8430 at 20iterations 2.936585 64.76582 at 30iterations 1.679830 38.16364 at 40iterations 0.9553890 20.24119 at 50iterations 0.5436878 11.28116 at 60iterations 0.3095590 6.000782 at 70iterations 0.1760104 3.726357 at 80iterations 0.1003537 2.065308 at 90iterations 5.7207976E-02 1.083687 at 100iterations 3.2570284E-02 0.6533804 at 110iterations 1.8557219E-02 0.3562393 at 120iterations 1.0645503E-02 0.2193451 at 130iterations 6.1789188E-03 0.1204796 at 140iterations 3.6381730E-03 7.5103760E-02 at 150iterations 2.2152008E-03 4.9255371E-02 at 160iterations 1.4163584E-03 3.1967163E-02 at 170iterations 9.6729532E-04 2.4276733E-02 at 180iterations finished qdiffx linear iterations at : 02:52:20 total time elapsed so far: 12.17000 # loops : 180 mean,max change (kT/e) : 9.6729532E-04 2.4276733E-02 energy calculations done at 12.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.31000 DelPhi exited at 02:52:21 12.312u 0.201s 0:12.78 97.8% 0+0k 0+0io 0pf+0w