Sun Oct 9 20:59:40 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 Sun Oct 9 2011 at 20:59:40 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3238 !!! WARNING: GLM 39 has a net charge of -0.6000 !!! WARNING: HIZ 43 has a net charge of 0.2000 !!! WARNING: SEP 139 has a net charge of -0.4750 !!! WARNING: CYS 258 has a net charge of 0.5000 !!! WARNING: GLM 421 has a net charge of -0.6000 !!! WARNING: GLM 555 has a net charge of -0.6000 !!! WARNING: HIZ 559 has a net charge of 0.2000 !!! WARNING: ZN7 775 has a net charge of 1.4000 !!! WARNING: ZN7 779 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6353171 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): 45.30000 98.37800 ymin,ymax (A): 2.976000 59.01100 zmin,zma (A): 15.06100 67.42900 x,y,z range (A): 53.07800 56.03500 52.36800 scale (grids/A): 0.6353171 object centre (A): 71.83900 30.99350 41.24500 number of atom coordinates read : 3238 total number of charged atoms : 3086 net assigned charge : 6.925013 assigned positive charge : 494.0276 centred at (gu) : 90.40534 88.02292 90.51275 assigned negative charge : -487.1041 centred at (gu) : 90.31828 87.96789 90.54739 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8932 nv = 96 ne = 84 npr = 63439 no. pairs analyzed = 63439 no. exposed pairs = 4225 no. arc points = 30694 no. surface atoms = 1408 nbur = 1830 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 442 mr = 4707 m= 3 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 41 time to turn everything in is 0.3200000 number of dielectric boundary points 4628 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3031 ## 300 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 10718 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1957046E-08 4.9191646E-09 midg,1,midg; midg,igrid,midg 2.4848268E-09 1.0491925E-08 1,midg,midg; igrid,midg,midg -2.1201394E-09 2.1768386E-08 gauss-seidel spectral radius is 0.9872317 estimated iterations to convergence 72 setup time was (sec) 0.5400000 now iterating at: 20:59:41 rms-change max change #iterations 0.1610515 31.00920 at 10iterations 1.5472036E-02 2.697357 at 20iterations 1.5230072E-03 0.2251129 at 30iterations 1.5247184E-04 2.0984650E-02 at 40iterations 1.8014922E-05 2.1209717E-03 at 50iterations finished qdiffx linear iterations at : 20:59:43 total time elapsed so far: 2.960000 # loops : 50 mean,max change (kT/e) : 1.8014922E-05 2.1209717E-03 energy calculations done at 2.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.130000 DelPhi exited at 20:59:43 3.137u 0.138s 0:03.55 91.8% 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 20:59:44 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3238 !!! WARNING: GLM 39 has a net charge of -0.6000 !!! WARNING: HIZ 43 has a net charge of 0.2000 !!! WARNING: SEP 139 has a net charge of -0.4750 !!! WARNING: CYS 258 has a net charge of 0.5000 !!! WARNING: GLM 421 has a net charge of -0.6000 !!! WARNING: GLM 555 has a net charge of -0.6000 !!! WARNING: HIZ 559 has a net charge of 0.2000 !!! WARNING: ZN7 775 has a net charge of 1.4000 !!! WARNING: ZN7 779 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.905951 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): 45.30000 98.37800 ymin,ymax (A): 2.976000 59.01100 zmin,zma (A): 15.06100 67.42900 x,y,z range (A): 53.07800 56.03500 52.36800 scale (grids/A): 1.905951 object centre (A): 71.83900 30.99350 41.24500 number of atom coordinates read : 3238 total number of charged atoms : 3086 net assigned charge : 6.925013 assigned positive charge : 494.0276 centred at (gu) : 91.21545 84.06792 91.53715 assigned negative charge : -487.1041 centred at (gu) : 90.95438 83.90325 91.64188 start vw surface at 0.1800000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 95719 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30694 grid for indexing accessible points = 1.400000 m= 33119 mr = 64796 m= 5147 mr = 23486 m= 322 mr = 2941 m= 4 mr = 97 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 3177 time to turn everything in is 0.6400000 number of dielectric boundary points 42991 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 203 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 24241 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) : 0.6353171 object centre at (A) : 71.83900 30.99350 41.24500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.9140669E-03 -1.6032077E-02 midg,1,midg; midg,igrid,midg 9.6688777E-02 3.8795013E-02 1,midg,midg; igrid,midg,midg -2.1713406E-02 2.6721744E-02 gauss-seidel spectral radius is 0.9987125 estimated iterations to convergence 221 setup time was (sec) 0.9100000 now iterating at: 20:59:45 rms-change max change #iterations 4.866115 184.7416 at 10iterations 2.320813 66.64468 at 20iterations 1.109351 33.19044 at 30iterations 0.5285176 16.59034 at 40iterations 0.2521572 7.419083 at 50iterations 0.1209223 3.678696 at 60iterations 5.7829052E-02 1.773941 at 70iterations 2.7686233E-02 0.7730598 at 80iterations 1.3200052E-02 0.3884277 at 90iterations 6.3211434E-03 0.2000016 at 100iterations 3.0201732E-03 9.5155716E-02 at 110iterations 1.4485819E-03 3.9347649E-02 at 120iterations finished qdiffx linear iterations at : 20:59:51 total time elapsed so far: 6.910000 # loops : 120 mean,max change (kT/e) : 1.4485819E-03 3.9347649E-02 energy calculations done at 6.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.080000 DelPhi exited at 20:59:51 7.083u 0.150s 0:07.58 95.3% 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 Sun Oct 9 2011 at 20:59:51 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3238 !!! WARNING: GLM 39 has a net charge of -0.6000 !!! WARNING: HIZ 43 has a net charge of 0.2000 !!! WARNING: SEP 139 has a net charge of -0.4750 !!! WARNING: CYS 258 has a net charge of 0.5000 !!! WARNING: GLM 421 has a net charge of -0.6000 !!! WARNING: GLM 555 has a net charge of -0.6000 !!! WARNING: HIZ 559 has a net charge of 0.2000 !!! WARNING: ZN7 775 has a net charge of 1.4000 !!! WARNING: ZN7 779 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.858927 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): 45.30000 98.37800 ymin,ymax (A): 2.976000 59.01100 zmin,zma (A): 15.06100 67.42900 x,y,z range (A): 53.07800 56.03500 52.36800 scale (grids/A): 2.858927 object centre (A): 71.83900 30.99350 41.24500 number of atom coordinates read : 3238 total number of charged atoms : 3086 net assigned charge : 6.925013 assigned positive charge : 494.0276 centred at (gu) : 91.82288 81.10163 92.30552 assigned negative charge : -487.1041 centred at (gu) : 91.43152 80.85479 92.46284 start vw surface at 0.1600000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 221430 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30694 grid for indexing accessible points = 1.400000 m= 108092 mr = 157310 m= 37475 mr = 86692 m= 8952 mr = 29066 m= 1353 mr = 6303 m= 93 mr = 860 m= 3 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.9499999 no. cavity mid-points inaccessible to solvent = 10756 time to turn everything in is 1.590000 number of dielectric boundary points 97117 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.720000 number of grid points assigned charge 24684 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) : 1.905951 object centre at (A) : 71.83900 30.99350 41.24500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1201052 -0.3240409 midg,1,midg; midg,igrid,midg 0.8361650 0.4000995 1,midg,midg; igrid,midg,midg -0.2737884 0.3104449 gauss-seidel spectral radius is 0.9993027 estimated iterations to convergence 299 setup time was (sec) 1.880000 now iterating at: 20:59:53 rms-change max change #iterations 11.59691 326.7615 at 10iterations 6.997931 176.1630 at 20iterations 4.199978 104.9265 at 30iterations 2.506115 47.72069 at 40iterations 1.486985 30.30147 at 50iterations 0.8783197 15.98408 at 60iterations 0.5198444 9.294526 at 70iterations 0.3059798 5.514337 at 80iterations 0.1797427 3.303643 at 90iterations 0.1057043 2.058638 at 100iterations 6.2158052E-02 1.022392 at 110iterations 3.6431294E-02 0.5836948 at 120iterations 2.1409631E-02 0.3522339 at 130iterations 1.2532869E-02 0.2184563 at 140iterations 7.3494590E-03 0.1339989 at 150iterations 4.3030065E-03 6.9068909E-02 at 160iterations 2.5237983E-03 3.9325714E-02 at 170iterations 1.4802739E-03 2.5380135E-02 at 180iterations finished qdiffx linear iterations at : 21:00:03 total time elapsed so far: 11.63000 # loops : 180 mean,max change (kT/e) : 1.4802739E-03 2.5380135E-02 energy calculations done at 11.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.81000 DelPhi exited at 21:00:03 11.810u 0.173s 0:12.25 97.7% 0+0k 0+0io 0pf+0w