Mon Oct 10 14:11:56 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 Mon Oct 10 2011 at 14:11:56 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 = 2106 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: 0.6373304 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): -13.21400 41.04000 ymin,ymax (A): -31.96400 23.89400 zmin,zma (A): -9.653001 32.62100 x,y,z range (A): 54.25400 55.85800 42.27400 scale (grids/A): 0.6373304 object centre (A): 13.91300 -4.035000 11.48400 number of atom coordinates read : 2106 total number of charged atoms : 1974 net assigned charge : 11.50002 assigned positive charge : 303.0549 centred at (gu) : 88.68935 91.86829 91.68524 assigned negative charge : -291.5553 centred at (gu) : 88.71943 91.94157 91.66027 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6101 nv = 96 ne = 84 npr = 41206 no. pairs analyzed = 41206 no. exposed pairs = 2869 no. arc points = 20570 no. surface atoms = 965 nbur = 1141 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 376 mr = 3133 m= 2 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3309 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2051 ## 179 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7065 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.5076507E-09 2.4859343E-08 midg,1,midg; midg,igrid,midg 1.4427423E-08 1.3785899E-08 1,midg,midg; igrid,midg,midg 2.3505370E-08 9.9427391E-09 gauss-seidel spectral radius is 0.9872147 estimated iterations to convergence 72 setup time was (sec) 0.5500000 now iterating at: 14:11:57 rms-change max change #iterations 0.1198916 21.76571 at 10iterations 1.1815821E-02 2.017988 at 20iterations 1.2029712E-03 0.1821022 at 30iterations 1.7690271E-04 2.7042389E-02 at 40iterations 4.2986234E-05 6.9971085E-03 at 50iterations finished qdiffx linear iterations at : 14:12:00 total time elapsed so far: 3.920000 # loops : 50 mean,max change (kT/e) : 4.2986234E-05 6.9971085E-03 energy calculations done at 3.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.100000 DelPhi exited at 14:12:01 4.100u 0.225s 0:04.62 93.5% 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 Mon Oct 10 2011 at 14:12:01 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 = 2106 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: 1.911991 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): -13.21400 41.04000 ymin,ymax (A): -31.96400 23.89400 zmin,zma (A): -9.653001 32.62100 x,y,z range (A): 54.25400 55.85800 42.27400 scale (grids/A): 1.911991 object centre (A): 13.91300 -4.035000 11.48400 number of atom coordinates read : 2106 total number of charged atoms : 1974 net assigned charge : 11.50002 assigned positive charge : 303.0549 centred at (gu) : 86.06793 95.60474 95.05542 assigned negative charge : -291.5553 centred at (gu) : 86.15855 95.82489 94.98074 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 64940 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20570 grid for indexing accessible points = 1.400000 m= 24125 mr = 43211 m= 4256 mr = 17465 m= 275 mr = 2656 m= 2 mr = 100 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 0.5300000 number of dielectric boundary points 30166 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 152 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 15544 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) : 0.6373304 object centre at (A) : 13.91300 -4.035000 11.48400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.6230220E-04 2.4347713E-02 midg,1,midg; midg,igrid,midg 4.0308967E-02 3.0584650E-02 1,midg,midg; igrid,midg,midg 5.6899883E-02 3.1280309E-02 gauss-seidel spectral radius is 0.9986031 estimated iterations to convergence 212 setup time was (sec) 0.8400000 now iterating at: 14:12:02 rms-change max change #iterations 3.629988 181.4494 at 10iterations 1.678072 65.78442 at 20iterations 0.7766123 28.53585 at 30iterations 0.3584200 12.54533 at 40iterations 0.1663211 5.774897 at 50iterations 7.7122129E-02 2.571656 at 60iterations 3.5695530E-02 1.420248 at 70iterations 1.6537178E-02 0.5419025 at 80iterations 7.6993019E-03 0.2570645 at 90iterations 3.5771176E-03 0.1211166 at 100iterations 1.6769127E-03 5.6653023E-02 at 110iterations 7.8828243E-04 2.6101112E-02 at 120iterations finished qdiffx linear iterations at : 14:12:10 total time elapsed so far: 9.130000 # loops : 120 mean,max change (kT/e) : 7.8828243E-04 2.6101112E-02 energy calculations done at 9.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.300000 DelPhi exited at 14:12:10 9.307u 0.243s 0:09.90 96.3% 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 Mon Oct 10 2011 at 14:12:11 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2106 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: 2.867987 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): -13.21400 41.04000 ymin,ymax (A): -31.96400 23.89400 zmin,zma (A): -9.653001 32.62100 x,y,z range (A): 54.25400 55.85800 42.27400 scale (grids/A): 2.867987 object centre (A): 13.91300 -4.035000 11.48400 number of atom coordinates read : 2106 total number of charged atoms : 1974 net assigned charge : 11.50002 assigned positive charge : 303.0549 centred at (gu) : 84.10180 98.40706 97.58328 assigned negative charge : -291.5553 centred at (gu) : 84.23793 98.73731 97.47112 start vw surface at 0.1400000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 149788 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20570 grid for indexing accessible points = 1.400000 m= 76419 mr = 105032 m= 28960 mr = 61509 m= 7680 mr = 23097 m= 1179 mr = 5751 m= 63 mr = 777 m= 0 mr = 15 time to grow re-entrant surface = 0.7600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.300000 number of dielectric boundary points 67908 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.450000 number of grid points assigned charge 15792 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) : 1.911991 object centre at (A) : 13.91300 -4.035000 11.48400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.9481706E-03 0.2613608 midg,1,midg; midg,igrid,midg 0.4725102 0.3516356 1,midg,midg; igrid,midg,midg 0.5814915 0.2882295 gauss-seidel spectral radius is 0.9992514 estimated iterations to convergence 288 setup time was (sec) 1.640000 now iterating at: 14:12:12 rms-change max change #iterations 8.758328 346.7834 at 10iterations 5.157731 135.4343 at 20iterations 3.010208 77.68933 at 30iterations 1.754082 39.27452 at 40iterations 1.015148 25.86525 at 50iterations 0.5867996 12.53685 at 60iterations 0.3391657 7.866464 at 70iterations 0.1954992 4.342758 at 80iterations 0.1126195 2.333503 at 90iterations 6.4837731E-02 1.381149 at 100iterations 3.7259810E-02 0.8546295 at 110iterations 2.1449834E-02 0.4371109 at 120iterations 1.2323132E-02 0.2663383 at 130iterations 7.0530819E-03 0.1479216 at 140iterations 4.0627979E-03 8.0864906E-02 at 150iterations 2.3406707E-03 4.6014786E-02 at 160iterations 1.3510736E-03 2.6057720E-02 at 170iterations 7.8113016E-04 1.5324295E-02 at 180iterations finished qdiffx linear iterations at : 14:12:25 total time elapsed so far: 14.68000 # loops : 180 mean,max change (kT/e) : 7.8113016E-04 1.5324295E-02 energy calculations done at 14.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.86000 DelPhi exited at 14:12:26 14.861u 0.247s 0:15.49 97.4% 0+0k 0+0io 0pf+0w