Sun Oct 9 06:33:37 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 06:33:37 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1946 !!! WARNING: GLM 35 has a net charge of -0.0940 !!! WARNING: ASP 186 has a net charge of -2.0000 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: 0.7021696 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): -22.00000 23.64200 ymin,ymax (A): 14.26400 59.05300 zmin,zma (A): -20.70100 29.99900 x,y,z range (A): 45.64200 44.78900 50.70000 scale (grids/A): 0.7021696 object centre (A): 0.8210001 36.65850 4.649000 number of atom coordinates read : 1946 total number of charged atoms : 1803 net assigned charge : 0.4060155 assigned positive charge : 289.9430 centred at (gu) : 89.72836 89.19272 90.56532 assigned negative charge : -289.5371 centred at (gu) : 89.79134 89.38852 90.43613 start vw surface at 5.9999999E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 6555 nv = 96 ne = 84 npr = 40004 no. pairs analyzed = 40004 no. exposed pairs = 2498 no. arc points = 17874 no. surface atoms = 840 nbur = 1106 mkacc time = 7.0000000E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 414 mr = 3550 m= 4 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 8.0000006E-02 no. cavity mid-points inaccessible to solvent = 31 time to turn everything in is 0.1500000 number of dielectric boundary points 3350 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1672 ## 142 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 7240 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.5805479E-08 6.0487459E-08 midg,1,midg; midg,igrid,midg 9.4447138E-08 -6.7502327E-08 1,midg,midg; igrid,midg,midg 2.9059075E-08 -2.2539620E-08 gauss-seidel spectral radius is 0.9894246 estimated iterations to convergence 79 setup time was (sec) 0.3400000 now iterating at: 06:33:38 rms-change max change #iterations 0.1838312 28.30373 at 10iterations 2.2299001E-02 3.273581 at 20iterations 2.7127031E-03 0.4411774 at 30iterations 3.2552538E-04 4.5043945E-02 at 40iterations 3.9403123E-05 5.9719086E-03 at 50iterations finished qdiffx linear iterations at : 06:33:41 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 3.9403123E-05 5.9719086E-03 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 06:33:41 3.323u 0.184s 0:03.80 92.1% 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 06:33:41 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1946 !!! WARNING: GLM 35 has a net charge of -0.0940 !!! WARNING: ASP 186 has a net charge of -2.0000 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: 2.106509 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): -22.00000 23.64200 ymin,ymax (A): 14.26400 59.05300 zmin,zma (A): -20.70100 29.99900 x,y,z range (A): 45.64200 44.78900 50.70000 scale (grids/A): 2.106509 object centre (A): 0.8210001 36.65850 4.649000 number of atom coordinates read : 1946 total number of charged atoms : 1803 net assigned charge : 0.4060155 assigned positive charge : 289.9430 centred at (gu) : 89.18496 87.57801 91.69597 assigned negative charge : -289.5371 centred at (gu) : 89.37426 88.16559 91.30831 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 68954 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17874 grid for indexing accessible points = 1.400000 m= 26778 mr = 46633 m= 5267 mr = 20282 m= 488 mr = 3594 m= 8 mr = 242 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 845 time to turn everything in is 0.3500000 number of dielectric boundary points 30744 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 64 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 14316 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) : 0.7021696 object centre at (A) : 0.8210001 36.65850 4.649000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2565284E-02 -1.3303304E-02 midg,1,midg; midg,igrid,midg 6.9933787E-02 -3.7753496E-02 1,midg,midg; igrid,midg,midg 1.4390743E-02 -8.7352470E-03 gauss-seidel spectral radius is 0.9988146 estimated iterations to convergence 230 setup time was (sec) 0.5700000 now iterating at: 06:33:42 rms-change max change #iterations 4.383320 194.0844 at 10iterations 2.138641 77.02318 at 20iterations 1.055757 35.33382 at 30iterations 0.5212096 16.07192 at 40iterations 0.2557367 7.871999 at 50iterations 0.1262970 4.297638 at 60iterations 6.2150724E-02 2.080152 at 70iterations 3.0664900E-02 0.9728222 at 80iterations 1.5072526E-02 0.4628448 at 90iterations 7.4199494E-03 0.2354050 at 100iterations 3.6632977E-03 0.1145439 at 110iterations 1.8055249E-03 5.6356430E-02 at 120iterations finished qdiffx linear iterations at : 06:33:49 total time elapsed so far: 7.560000 # loops : 120 mean,max change (kT/e) : 1.8055249E-03 5.6356430E-02 energy calculations done at 7.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.680000 DelPhi exited at 06:33:49 7.684u 0.203s 0:08.20 96.0% 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 Sun Oct 9 2011 at 06:33:49 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1946 !!! WARNING: GLM 35 has a net charge of -0.0940 !!! WARNING: ASP 186 has a net charge of -2.0000 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: 3.159763 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): -22.00000 23.64200 ymin,ymax (A): 14.26400 59.05300 zmin,zma (A): -20.70100 29.99900 x,y,z range (A): 45.64200 44.78900 50.70000 scale (grids/A): 3.159763 object centre (A): 0.8210001 36.65850 4.649000 number of atom coordinates read : 1946 total number of charged atoms : 1803 net assigned charge : 0.4060155 assigned positive charge : 289.9430 centred at (gu) : 88.77752 86.36699 92.54395 assigned negative charge : -289.5371 centred at (gu) : 89.06132 87.24844 91.96242 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 158737 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17874 grid for indexing accessible points = 1.400000 m= 82611 mr = 112459 m= 34435 mr = 68117 m= 10093 mr = 28720 m= 1962 mr = 7923 m= 253 mr = 1457 m= 5 mr = 163 m= 0 mr = 2 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 2823 time to turn everything in is 1.050000 number of dielectric boundary points 69255 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.130000 number of grid points assigned charge 14424 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) : 2.106509 object centre at (A) : 0.8210001 36.65850 4.649000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.7293028E-02 -0.2230206 midg,1,midg; midg,igrid,midg 0.7267163 -0.2695617 1,midg,midg; igrid,midg,midg 0.1921648 -6.2896416E-02 gauss-seidel spectral radius is 0.9992953 estimated iterations to convergence 297 setup time was (sec) 1.270000 now iterating at: 06:33:51 rms-change max change #iterations 9.890666 451.6465 at 10iterations 5.792877 120.9039 at 20iterations 3.374198 66.26354 at 30iterations 1.971228 33.57743 at 40iterations 1.148319 20.41181 at 50iterations 0.6679091 13.37802 at 60iterations 0.3894001 8.319630 at 70iterations 0.2265321 3.924041 at 80iterations 0.1315149 2.456844 at 90iterations 7.6615281E-02 1.433723 at 100iterations 4.4555850E-02 0.8051529 at 110iterations 2.5852626E-02 0.4492874 at 120iterations 1.5033098E-02 0.2547531 at 130iterations 8.7381955E-03 0.1591911 at 140iterations 5.0850110E-03 9.0739250E-02 at 150iterations 2.9570013E-03 5.9607133E-02 at 160iterations 1.7207050E-03 2.9199600E-02 at 170iterations 9.9944579E-04 1.7578125E-02 at 180iterations finished qdiffx linear iterations at : 06:34:02 total time elapsed so far: 12.41000 # loops : 180 mean,max change (kT/e) : 9.9944579E-04 1.7578125E-02 energy calculations done at 12.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.55000 DelPhi exited at 06:34:02 12.551u 0.205s 0:13.02 97.9% 0+0k 0+0io 0pf+0w