Tue Nov 22 14:12:30 PST 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 Tue Nov 22 2011 at 14:12:34 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 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: 0.6363052 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): -4.416000 35.11800 ymin,ymax (A): -3.783000 47.77600 zmin,zma (A): -23.90100 32.04700 x,y,z range (A): 39.53400 51.55900 55.94800 scale (grids/A): 0.6363052 object centre (A): 15.35100 21.99650 4.073001 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 292.1999 centred at (gu) : 90.31049 92.75504 89.71811 assigned negative charge : -289.2002 centred at (gu) : 90.41579 92.88972 89.65263 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5456 nv = 96 ne = 84 npr = 40113 no. pairs analyzed = 40113 no. exposed pairs = 2509 no. arc points = 17579 no. surface atoms = 852 nbur = 1118 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 270 mr = 2951 m= 0 mr = 37 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 37 time to turn everything in is 0.2300000 number of dielectric boundary points 2738 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1815 ## 176 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 6473 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.2310470E-10 8.7861443E-09 midg,1,midg; midg,igrid,midg 8.1289739E-09 -1.2006033E-08 1,midg,midg; igrid,midg,midg 1.1573195E-08 -4.3097810E-09 gauss-seidel spectral radius is 0.9871511 estimated iterations to convergence 72 setup time was (sec) 0.4700000 now iterating at: 14:12:37 rms-change max change #iterations 0.1204966 24.98171 at 10iterations 1.1861621E-02 1.984482 at 20iterations 1.1523376E-03 0.2046003 at 30iterations 1.1051671E-04 1.7623901E-02 at 40iterations 1.0711605E-05 1.9798279E-03 at 50iterations finished qdiffx linear iterations at : 14:12:45 total time elapsed so far: 3.080000 # loops : 50 mean,max change (kT/e) : 1.0711605E-05 1.9798279E-03 energy calculations done at 3.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.260000 DelPhi exited at 14:12:46 3.261u 0.162s 0:12.08 28.3% 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 Tue Nov 22 2011 at 14:12:47 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 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: 1.908916 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): -4.416000 35.11800 ymin,ymax (A): -3.783000 47.77600 zmin,zma (A): -23.90100 32.04700 x,y,z range (A): 39.53400 51.55900 55.94800 scale (grids/A): 1.908916 object centre (A): 15.35100 21.99650 4.073001 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 292.1999 centred at (gu) : 90.93134 98.26521 89.15417 assigned negative charge : -289.2002 centred at (gu) : 91.24731 98.66952 88.95798 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 57930 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17579 grid for indexing accessible points = 1.400000 m= 21884 mr = 39367 m= 3430 mr = 16537 m= 153 mr = 2247 m= 3 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 898 time to turn everything in is 0.4200000 number of dielectric boundary points 25215 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 135 iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 14475 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) : 0.6363052 object centre at (A) : 15.35100 21.99650 4.073001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7781482E-02 7.7857096E-03 midg,1,midg; midg,igrid,midg 3.2941844E-02 -4.9036737E-03 1,midg,midg; igrid,midg,midg 1.0657488E-02 -4.3220008E-03 gauss-seidel spectral radius is 0.9985654 estimated iterations to convergence 209 setup time was (sec) 0.7100000 now iterating at: 14:12:49 rms-change max change #iterations 3.592772 174.7083 at 10iterations 1.644890 61.58354 at 20iterations 0.7576437 27.62649 at 30iterations 0.3471107 11.58639 at 40iterations 0.1596113 5.556595 at 50iterations 7.3203482E-02 2.444493 at 60iterations 3.3571314E-02 1.233220 at 70iterations 1.5404408E-02 0.5617224 at 80iterations 7.0717088E-03 0.2577896 at 90iterations 3.2563561E-03 0.1176033 at 100iterations 1.4901281E-03 5.9204102E-02 at 110iterations 6.8827753E-04 2.8414488E-02 at 120iterations finished qdiffx linear iterations at : 14:13:05 total time elapsed so far: 7.490000 # loops : 120 mean,max change (kT/e) : 6.8827753E-04 2.8414488E-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) 7.660000 DelPhi exited at 14:13:07 7.666u 0.318s 0:19.88 40.0% 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 Nov 22 2011 at 14:13:08 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 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: 2.863373 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): -4.416000 35.11800 ymin,ymax (A): -3.783000 47.77600 zmin,zma (A): -23.90100 32.04700 x,y,z range (A): 39.53400 51.55900 55.94800 scale (grids/A): 2.863373 object centre (A): 15.35100 21.99650 4.073001 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 292.1999 centred at (gu) : 91.39697 102.3977 88.73123 assigned negative charge : -289.2002 centred at (gu) : 91.87103 103.0042 88.43696 start vw surface at 0.1100000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 133235 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17579 grid for indexing accessible points = 1.400000 m= 69136 mr = 94813 m= 26650 mr = 57103 m= 6140 mr = 22075 m= 722 mr = 4683 m= 27 mr = 437 m= 0 mr = 4 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 2924 time to turn everything in is 1.040000 number of dielectric boundary points 56795 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 14704 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) : 1.908916 object centre at (A) : 15.35100 21.99650 4.073001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.115415 -1.0612992E-02 midg,1,midg; midg,igrid,midg 0.3898192 -0.1302989 1,midg,midg; igrid,midg,midg 8.0569737E-02 -2.3891054E-02 gauss-seidel spectral radius is 0.9992282 estimated iterations to convergence 284 setup time was (sec) 1.330000 now iterating at: 14:13:11 rms-change max change #iterations 8.494715 494.0097 at 10iterations 4.868669 117.6486 at 20iterations 2.778938 64.44720 at 30iterations 1.584122 33.53803 at 40iterations 0.9001128 20.30617 at 50iterations 0.5124815 11.47331 at 60iterations 0.2915471 5.928726 at 70iterations 0.1651224 3.450399 at 80iterations 9.3823448E-02 1.931400 at 90iterations 5.3292219E-02 1.082787 at 100iterations 3.0125244E-02 0.6673126 at 110iterations 1.7071083E-02 0.3311920 at 120iterations 9.6846819E-03 0.1944542 at 130iterations 5.4812632E-03 0.1054382 at 140iterations 3.1104810E-03 6.1860085E-02 at 150iterations 1.7652756E-03 3.4516335E-02 at 160iterations 1.0020905E-03 2.0776749E-02 at 170iterations 5.6772039E-04 1.1022568E-02 at 180iterations finished qdiffx linear iterations at : 14:13:34 total time elapsed so far: 10.90000 # loops : 180 mean,max change (kT/e) : 5.6772039E-04 1.1022568E-02 energy calculations done at 10.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.08000 DelPhi exited at 14:13:35 11.079u 0.185s 0:26.94 41.7% 0+0k 0+0io 0pf+0w