Sat Oct 8 11:34:13 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 Sat Oct 8 2011 at 11:34:13 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2371 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: 0.6627448 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): -59.57500 -11.52700 ymin,ymax (A): 54.12400 102.2870 zmin,zma (A): 38.44100 92.15700 x,y,z range (A): 48.04800 48.16300 53.71600 scale (grids/A): 0.6627448 object centre (A): -35.55100 78.20551 65.29900 number of atom coordinates read : 2371 total number of charged atoms : 2224 net assigned charge : -0.9999913 assigned positive charge : 345.3781 centred at (gu) : 91.47122 90.44371 91.87510 assigned negative charge : -346.3785 centred at (gu) : 91.42877 90.36663 91.93182 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7240 nv = 96 ne = 84 npr = 47474 no. pairs analyzed = 47474 no. exposed pairs = 3067 no. arc points = 21681 no. surface atoms = 1045 nbur = 1326 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 390 mr = 3883 m= 1 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3702 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2059 ## 172 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8312 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.3130806E-09 -1.9976035E-08 midg,1,midg; midg,igrid,midg -1.5780163E-08 1.2869529E-08 1,midg,midg; igrid,midg,midg -7.9048315E-09 7.2717965E-09 gauss-seidel spectral radius is 0.9881880 estimated iterations to convergence 75 setup time was (sec) 0.4700000 now iterating at: 11:34:14 rms-change max change #iterations 0.1607044 23.44912 at 10iterations 1.7610282E-02 2.461639 at 20iterations 1.8573555E-03 0.2286320 at 30iterations 2.0039469E-04 2.5913239E-02 at 40iterations 2.1746013E-05 2.9811859E-03 at 50iterations finished qdiffx linear iterations at : 11:34:17 total time elapsed so far: 4.210000 # loops : 50 mean,max change (kT/e) : 2.1746013E-05 2.9811859E-03 energy calculations done at 4.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.350000 DelPhi exited at 11:34:18 4.354u 0.299s 0:04.93 94.1% 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 Sat Oct 8 2011 at 11:34:18 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2371 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: 1.988234 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): -59.57500 -11.52700 ymin,ymax (A): 54.12400 102.2870 zmin,zma (A): 38.44100 92.15700 x,y,z range (A): 48.04800 48.16300 53.71600 scale (grids/A): 1.988234 object centre (A): -35.55100 78.20551 65.29900 number of atom coordinates read : 2371 total number of charged atoms : 2224 net assigned charge : -0.9999913 assigned positive charge : 345.3781 centred at (gu) : 94.41318 91.33057 95.62479 assigned negative charge : -346.3785 centred at (gu) : 94.28603 91.09960 95.79530 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 78000 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21681 grid for indexing accessible points = 1.400000 m= 27919 mr = 53344 m= 4498 mr = 20393 m= 288 mr = 2758 m= 2 mr = 112 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.4200000 number of dielectric boundary points 34100 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 106 iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 17572 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) : 0.6627448 object centre at (A) : -35.55100 78.20551 65.29900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8289681E-02 -1.5112503E-03 midg,1,midg; midg,igrid,midg -1.8170789E-02 -6.5964428E-03 1,midg,midg; igrid,midg,midg -1.1054646E-02 2.3154920E-02 gauss-seidel spectral radius is 0.9987242 estimated iterations to convergence 222 setup time was (sec) 0.7400000 now iterating at: 11:34:19 rms-change max change #iterations 4.335844 172.3136 at 10iterations 2.078832 77.20866 at 20iterations 0.9969664 30.05580 at 30iterations 0.4769695 14.02007 at 40iterations 0.2297542 6.841880 at 50iterations 0.1101370 3.405503 at 60iterations 5.2826650E-02 1.699883 at 70iterations 2.5413066E-02 0.7512360 at 80iterations 1.2193152E-02 0.3839402 at 90iterations 5.8431905E-03 0.1791143 at 100iterations 2.8050072E-03 8.2912445E-02 at 110iterations 1.3433401E-03 4.4170737E-02 at 120iterations finished qdiffx linear iterations at : 11:34:29 total time elapsed so far: 9.540000 # loops : 120 mean,max change (kT/e) : 1.3433401E-03 4.4170737E-02 energy calculations done at 9.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.680000 DelPhi exited at 11:34:29 9.681u 0.399s 0:11.45 87.9% 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 Sat Oct 8 2011 at 11:34:29 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2371 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: 2.982352 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): -59.57500 -11.52700 ymin,ymax (A): 54.12400 102.2870 zmin,zma (A): 38.44100 92.15700 x,y,z range (A): 48.04800 48.16300 53.71600 scale (grids/A): 2.982352 object centre (A): -35.55100 78.20551 65.29900 number of atom coordinates read : 2371 total number of charged atoms : 2224 net assigned charge : -0.9999913 assigned positive charge : 345.3781 centred at (gu) : 96.61951 91.99578 98.43713 assigned negative charge : -346.3785 centred at (gu) : 96.42900 91.64940 98.69287 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 180145 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21681 grid for indexing accessible points = 1.400000 m= 89751 mr = 129374 m= 32838 mr = 72935 m= 8065 mr = 26180 m= 1249 mr = 5987 m= 71 mr = 807 m= 1 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 59 time to turn everything in is 1.130000 number of dielectric boundary points 76808 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.290000 number of grid points assigned charge 17791 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) : 1.988234 object centre at (A) : -35.55100 78.20551 65.29900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3287119 -4.8960578E-02 midg,1,midg; midg,igrid,midg -0.1506233 -0.1197891 1,midg,midg; igrid,midg,midg -0.1445773 0.3037280 gauss-seidel spectral radius is 0.9992869 estimated iterations to convergence 295 setup time was (sec) 1.500000 now iterating at: 11:34:31 rms-change max change #iterations 10.09451 404.0063 at 10iterations 5.969973 143.4700 at 20iterations 3.518936 76.95953 at 30iterations 2.066815 39.87208 at 40iterations 1.205950 24.77958 at 50iterations 0.7059233 15.54707 at 60iterations 0.4118941 7.996394 at 70iterations 0.2404794 4.601878 at 80iterations 0.1398169 2.426034 at 90iterations 8.1390977E-02 1.417379 at 100iterations 4.7367826E-02 1.099394 at 110iterations 2.7536238E-02 0.5047531 at 120iterations 1.6003750E-02 0.3489075 at 130iterations 9.2810597E-03 0.1854649 at 140iterations 5.3931666E-03 0.1038818 at 150iterations 3.1299805E-03 5.6013346E-02 at 160iterations 1.8212737E-03 3.1440735E-02 at 170iterations 1.0577221E-03 1.8131256E-02 at 180iterations finished qdiffx linear iterations at : 11:34:45 total time elapsed so far: 15.51000 # loops : 180 mean,max change (kT/e) : 1.0577221E-03 1.8131256E-02 energy calculations done at 15.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.65000 DelPhi exited at 11:34:46 15.652u 0.384s 0:16.42 97.6% 0+0k 0+0io 0pf+0w