Sun Oct 9 18:57:14 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 18:57:14 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5098 !!! WARNING: ASL 284 has a net charge of -0.1000 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5700013 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): 3.237000 64.41800 ymin,ymax (A): -8.932000 53.14400 zmin,zma (A): -0.9730000 61.48300 x,y,z range (A): 61.18100 62.07600 62.45600 scale (grids/A): 0.5700013 object centre (A): 33.82750 22.10600 30.25500 number of atom coordinates read : 5098 total number of charged atoms : 4956 net assigned charge : -1.964944 assigned positive charge : 785.4517 centred at (gu) : 88.59317 89.34342 89.19254 assigned negative charge : -787.4227 centred at (gu) : 88.46027 89.36979 89.17310 start vw surface at 0.2200000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 10793 nv = 96 ne = 84 npr = 103765 no. pairs analyzed = 103765 no. exposed pairs = 5852 no. arc points = 39984 no. surface atoms = 1996 nbur = 3102 mkacc time = 0.3000000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 536 mr = 6313 m= 0 mr = 34 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 4982 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4035 ## 412 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 14118 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.4725994E-10 2.4219129E-10 midg,1,midg; midg,igrid,midg 5.7544114E-10 -8.3345592E-10 1,midg,midg; igrid,midg,midg -5.6157137E-09 2.4124325E-09 gauss-seidel spectral radius is 0.9842761 estimated iterations to convergence 66 setup time was (sec) 0.8700000 now iterating at: 18:57:15 rms-change max change #iterations 0.1255957 18.07065 at 10iterations 1.1175504E-02 1.744766 at 20iterations 2.5058945E-03 0.2700348 at 30iterations 1.0898674E-03 0.1325901 at 40iterations 5.0996646E-04 6.4978600E-02 at 50iterations finished qdiffx linear iterations at : 18:57:18 total time elapsed so far: 4.150000 # loops : 50 mean,max change (kT/e) : 5.0996646E-04 6.4978600E-02 energy calculations done at 4.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.330000 DelPhi exited at 18:57:19 4.333u 0.244s 0:04.86 94.0% 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 18:57:19 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5098 !!! WARNING: ASL 284 has a net charge of -0.1000 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.710004 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): 3.237000 64.41800 ymin,ymax (A): -8.932000 53.14400 zmin,zma (A): -0.9730000 61.48300 x,y,z range (A): 61.18100 62.07600 62.45600 scale (grids/A): 1.710004 object centre (A): 33.82750 22.10600 30.25500 number of atom coordinates read : 5098 total number of charged atoms : 4956 net assigned charge : -1.964944 assigned positive charge : 785.4517 centred at (gu) : 85.77791 88.02866 87.57641 assigned negative charge : -787.4227 centred at (gu) : 85.38100 88.10933 87.51917 start vw surface at 0.2300000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 121029 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39984 grid for indexing accessible points = 1.400000 m= 42809 mr = 88527 m= 5639 mr = 31538 m= 199 mr = 3200 m= 1 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 318 time to turn everything in is 1.040000 number of dielectric boundary points 46381 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 313 ## 1 charges are in solution ## iepsmp to db, and charging done at 1.180000 number of grid points assigned charge 38335 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) : 0.5700013 object centre at (A) : 33.82750 22.10600 30.25500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.7311807E-02 -2.6007311E-02 midg,1,midg; midg,igrid,midg 2.0149624E-02 9.6773887E-03 1,midg,midg; igrid,midg,midg -3.0691141E-02 2.8886799E-02 gauss-seidel spectral radius is 0.9985368 estimated iterations to convergence 207 setup time was (sec) 1.340000 now iterating at: 18:57:21 rms-change max change #iterations 5.180753 179.8097 at 10iterations 2.350661 69.96766 at 20iterations 1.078118 30.57998 at 30iterations 0.4936764 13.72385 at 40iterations 0.2257437 5.894188 at 50iterations 0.1034655 2.726797 at 60iterations 4.7574475E-02 1.342396 at 70iterations 2.1985773E-02 0.5828133 at 80iterations 1.0423313E-02 0.2932281 at 90iterations 5.1876060E-03 0.1429672 at 100iterations 2.8081469E-03 7.2177887E-02 at 110iterations 1.7342038E-03 4.8179626E-02 at 120iterations finished qdiffx linear iterations at : 18:57:29 total time elapsed so far: 9.900000 # loops : 120 mean,max change (kT/e) : 1.7342038E-03 4.8179626E-02 energy calculations done at 9.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.08000 DelPhi exited at 18:57:30 10.080u 0.284s 0:10.67 97.0% 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 18:57:30 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5098 !!! WARNING: ASL 284 has a net charge of -0.1000 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.565006 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): 3.237000 64.41800 ymin,ymax (A): -8.932000 53.14400 zmin,zma (A): -0.9730000 61.48300 x,y,z range (A): 61.18100 62.07600 62.45600 scale (grids/A): 2.565006 object centre (A): 33.82750 22.10600 30.25500 number of atom coordinates read : 5098 total number of charged atoms : 4956 net assigned charge : -1.964944 assigned positive charge : 785.4517 centred at (gu) : 83.66650 87.04258 86.36434 assigned negative charge : -787.4227 centred at (gu) : 83.07132 87.16415 86.27852 start vw surface at 0.2400000 fill in re-entrant regions at 0.8500000 boundary points on vw surface= 280910 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39984 grid for indexing accessible points = 1.400000 m= 143667 mr = 214527 m= 47000 mr = 118385 m= 9422 mr = 37194 m= 893 mr = 6671 m= 25 mr = 495 m= 0 mr = 3 time to grow re-entrant surface = 1.660000 no. cavity mid-points inaccessible to solvent = 1109 time to turn everything in is 2.670000 number of dielectric boundary points 104642 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 2.840000 number of grid points assigned charge 39628 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) : 1.710004 object centre at (A) : 33.82750 22.10600 30.25500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4923946 -0.6336154 midg,1,midg; midg,igrid,midg 7.0018873E-02 -1.1037272E-02 1,midg,midg; igrid,midg,midg -0.4910596 0.3159222 gauss-seidel spectral radius is 0.9992816 estimated iterations to convergence 294 setup time was (sec) 3.020000 now iterating at: 18:57:33 rms-change max change #iterations 12.83684 303.6937 at 10iterations 7.614158 172.8070 at 20iterations 4.486514 93.96133 at 30iterations 2.638831 46.59346 at 40iterations 1.545923 27.37751 at 50iterations 0.9034613 15.35228 at 60iterations 0.5279220 8.528624 at 70iterations 0.3074703 4.975273 at 80iterations 0.1789357 2.800831 at 90iterations 0.1043199 1.607658 at 100iterations 6.0737945E-02 0.9240112 at 110iterations 3.5479292E-02 0.5298615 at 120iterations 2.0763956E-02 0.3217545 at 130iterations 1.2290583E-02 0.2027283 at 140iterations 7.4061360E-03 0.1254272 at 150iterations 4.6053370E-03 7.3429108E-02 at 160iterations 3.0140930E-03 5.2274704E-02 at 170iterations 2.1129623E-03 3.5041809E-02 at 180iterations finished qdiffx linear iterations at : 18:57:48 total time elapsed so far: 17.63000 # loops : 180 mean,max change (kT/e) : 2.1129623E-03 3.5041809E-02 energy calculations done at 17.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.80000 DelPhi exited at 18:57:48 17.806u 0.306s 0:18.40 98.3% 0+0k 0+0io 0pf+0w