Sat Oct 8 23:18:39 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 23:18:39 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2201 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 0.6635230 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): -13.26400 40.38900 ymin,ymax (A): 14.12000 66.71000 zmin,zma (A): 1.812000 45.71200 x,y,z range (A): 53.65300 52.59000 43.90000 scale (grids/A): 0.6635230 object centre (A): 13.56250 40.41500 23.76200 number of atom coordinates read : 2201 total number of charged atoms : 2066 net assigned charge : 10.51402 assigned positive charge : 320.2517 centred at (gu) : 89.35732 88.37538 88.81435 assigned negative charge : -309.7382 centred at (gu) : 89.40409 88.37502 88.96449 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6951 nv = 96 ne = 84 npr = 43164 no. pairs analyzed = 43164 no. exposed pairs = 2922 no. arc points = 21482 no. surface atoms = 973 nbur = 1228 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 404 mr = 3674 m= 8 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 71 time to turn everything in is 0.1800000 number of dielectric boundary points 3642 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2039 ## 186 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7789 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.9354556E-08 2.3762918E-09 midg,1,midg; midg,igrid,midg 3.9957296E-08 2.0995017E-08 1,midg,midg; igrid,midg,midg 4.2015508E-08 1.8351953E-08 gauss-seidel spectral radius is 0.9882040 estimated iterations to convergence 75 setup time was (sec) 0.3800000 now iterating at: 23:18:40 rms-change max change #iterations 0.1544091 25.66401 at 10iterations 1.6375376E-02 2.323960 at 20iterations 1.7537898E-03 0.2233543 at 30iterations 2.0299529E-04 3.5369873E-02 at 40iterations 2.8334987E-05 4.0588379E-03 at 50iterations finished qdiffx linear iterations at : 23:18:43 total time elapsed so far: 3.470000 # loops : 50 mean,max change (kT/e) : 2.8334987E-05 4.0588379E-03 energy calculations done at 3.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.610000 DelPhi exited at 23:18:43 3.616u 0.210s 0:04.09 93.3% 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 Sat Oct 8 2011 at 23:18:43 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2201 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 1.990569 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): -13.26400 40.38900 ymin,ymax (A): 14.12000 66.71000 zmin,zma (A): 1.812000 45.71200 x,y,z range (A): 53.65300 52.59000 43.90000 scale (grids/A): 1.990569 object centre (A): 13.56250 40.41500 23.76200 number of atom coordinates read : 2201 total number of charged atoms : 2066 net assigned charge : 10.51402 assigned positive charge : 320.2517 centred at (gu) : 88.07175 85.12617 86.44281 assigned negative charge : -309.7382 centred at (gu) : 88.21222 85.12534 86.89377 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 73662 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21482 grid for indexing accessible points = 1.400000 m= 27743 mr = 49726 m= 4993 mr = 20303 m= 346 mr = 3214 m= 4 mr = 108 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 1866 time to turn everything in is 0.3700000 number of dielectric boundary points 33397 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 137 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 16353 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) : 0.6635230 object centre at (A) : 13.56250 40.41500 23.76200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8421627E-02 -1.1044618E-02 midg,1,midg; midg,igrid,midg 3.2090042E-02 4.3346643E-02 1,midg,midg; igrid,midg,midg 7.1387336E-02 2.3580974E-02 gauss-seidel spectral radius is 0.9987215 estimated iterations to convergence 222 setup time was (sec) 0.6100000 now iterating at: 23:18:44 rms-change max change #iterations 4.116745 196.4072 at 10iterations 1.968473 68.40216 at 20iterations 0.9396760 31.01326 at 30iterations 0.4491866 15.59803 at 40iterations 0.2159468 6.766010 at 50iterations 0.1033122 3.412241 at 60iterations 4.9653448E-02 1.532393 at 70iterations 2.3750918E-02 0.7429819 at 80iterations 1.1405845E-02 0.3558755 at 90iterations 5.4739830E-03 0.1791840 at 100iterations 2.6260526E-03 9.6050262E-02 at 110iterations 1.2633045E-03 4.4339180E-02 at 120iterations finished qdiffx linear iterations at : 23:18:52 total time elapsed so far: 8.240000 # loops : 120 mean,max change (kT/e) : 1.2633045E-03 4.4339180E-02 energy calculations done at 8.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.370000 DelPhi exited at 23:18:52 8.374u 0.260s 0:08.99 95.9% 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 23:18:52 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2201 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 2.985853 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): -13.26400 40.38900 ymin,ymax (A): 14.12000 66.71000 zmin,zma (A): 1.812000 45.71200 x,y,z range (A): 53.65300 52.59000 43.90000 scale (grids/A): 2.985853 object centre (A): 13.56250 40.41500 23.76200 number of atom coordinates read : 2201 total number of charged atoms : 2066 net assigned charge : 10.51402 assigned positive charge : 320.2517 centred at (gu) : 87.10764 82.68924 84.66412 assigned negative charge : -309.7382 centred at (gu) : 87.31827 82.68788 85.34077 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 169679 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21482 grid for indexing accessible points = 1.400000 m= 87105 mr = 120278 m= 33907 mr = 70588 m= 9252 mr = 27403 m= 1581 mr = 6981 m= 88 mr = 1037 m= 0 mr = 25 time to grow re-entrant surface = 0.5599999 no. cavity mid-points inaccessible to solvent = 5834 time to turn everything in is 0.9800000 number of dielectric boundary points 75300 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 16528 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) : 1.990569 object centre at (A) : 13.56250 40.41500 23.76200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3091760 -0.1203155 midg,1,midg; midg,igrid,midg 0.3271800 0.4512478 1,midg,midg; igrid,midg,midg 0.6668180 0.2098892 gauss-seidel spectral radius is 0.9992873 estimated iterations to convergence 296 setup time was (sec) 1.230000 now iterating at: 23:18:54 rms-change max change #iterations 9.652096 365.3057 at 10iterations 5.720430 132.2155 at 20iterations 3.378162 86.33371 at 30iterations 1.987136 43.63618 at 40iterations 1.167977 24.83679 at 50iterations 0.6841610 14.94115 at 60iterations 0.3998124 8.325472 at 70iterations 0.2333891 5.083903 at 80iterations 0.1363750 2.524729 at 90iterations 7.9263732E-02 1.775993 at 100iterations 4.6356276E-02 0.9071941 at 110iterations 2.6954275E-02 0.5257931 at 120iterations 1.5692446E-02 0.3326845 at 130iterations 9.1301594E-03 0.1758423 at 140iterations 5.3165732E-03 0.1010399 at 150iterations 3.0967793E-03 6.6362858E-02 at 160iterations 1.8131251E-03 3.6046028E-02 at 170iterations 1.0666657E-03 2.0854950E-02 at 180iterations finished qdiffx linear iterations at : 23:19:06 total time elapsed so far: 13.12000 # loops : 180 mean,max change (kT/e) : 1.0666657E-03 2.0854950E-02 energy calculations done at 13.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.26000 DelPhi exited at 23:19:06 13.261u 0.208s 0:13.75 97.8% 0+0k 0+0io 0pf+0w