Sun Oct 9 11:37:09 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 11:37:09 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2032 !!! WARNING: HIR 430 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6311162 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): -6.098000 38.88100 ymin,ymax (A): 5.456000 61.86400 zmin,zma (A): -15.46600 29.33400 x,y,z range (A): 44.97900 56.40800 44.80000 scale (grids/A): 0.6311162 object centre (A): 16.39150 33.66000 6.934000 number of atom coordinates read : 2032 total number of charged atoms : 1894 net assigned charge : 1.4007375E-02 assigned positive charge : 291.7658 centred at (gu) : 89.39405 92.72059 91.75883 assigned negative charge : -291.7523 centred at (gu) : 89.58672 92.65518 91.68191 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5593 nv = 96 ne = 84 npr = 40831 no. pairs analyzed = 40831 no. exposed pairs = 2878 no. arc points = 19937 no. surface atoms = 960 nbur = 1072 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 317 mr = 2736 m= 4 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 3146 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1904 ## 170 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 6537 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.7812713E-09 7.2228414E-09 midg,1,midg; midg,igrid,midg -2.6353031E-09 7.5712538E-09 1,midg,midg; igrid,midg,midg 1.4291445E-08 -1.1936362E-08 gauss-seidel spectral radius is 0.9869565 estimated iterations to convergence 72 setup time was (sec) 0.4600000 now iterating at: 11:37:09 rms-change max change #iterations 0.1132048 18.53507 at 10iterations 1.0761647E-02 1.761398 at 20iterations 1.0241856E-03 0.1726227 at 30iterations 9.7470765E-05 1.5583038E-02 at 40iterations 9.4545285E-06 1.8501282E-03 at 50iterations finished qdiffx linear iterations at : 11:37:12 total time elapsed so far: 3.040000 # loops : 50 mean,max change (kT/e) : 9.4545285E-06 1.8501282E-03 energy calculations done at 3.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.220000 DelPhi exited at 11:37:12 3.223u 0.212s 0:03.71 92.4% 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 11:37:12 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2032 !!! WARNING: HIR 430 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.893348 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): -6.098000 38.88100 ymin,ymax (A): 5.456000 61.86400 zmin,zma (A): -15.46600 29.33400 x,y,z range (A): 44.97900 56.40800 44.80000 scale (grids/A): 1.893348 object centre (A): 16.39150 33.66000 6.934000 number of atom coordinates read : 2032 total number of charged atoms : 1894 net assigned charge : 1.4007375E-02 assigned positive charge : 291.7658 centred at (gu) : 88.18191 98.16168 95.27636 assigned negative charge : -291.7523 centred at (gu) : 88.76031 97.96581 95.04588 start vw surface at 0.1300000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 59757 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19937 grid for indexing accessible points = 1.400000 m= 20875 mr = 38984 m= 3547 mr = 14401 m= 228 mr = 2170 m= 5 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 28805 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 111 iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 14926 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) : 0.6311162 object centre at (A) : 16.39150 33.66000 6.934000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.4857279E-03 6.9956058E-03 midg,1,midg; midg,igrid,midg 4.0740892E-03 2.5771072E-02 1,midg,midg; igrid,midg,midg 1.1497227E-02 -1.7375648E-02 gauss-seidel spectral radius is 0.9985722 estimated iterations to convergence 210 setup time was (sec) 0.7400000 now iterating at: 11:37:13 rms-change max change #iterations 3.573161 185.0040 at 10iterations 1.637144 74.14247 at 20iterations 0.7567035 27.37859 at 30iterations 0.3473848 13.39209 at 40iterations 0.1601297 5.958348 at 50iterations 7.3748663E-02 2.593786 at 60iterations 3.3890683E-02 1.121811 at 70iterations 1.5573854E-02 0.5311661 at 80iterations 7.1841897E-03 0.2881079 at 90iterations 3.2921783E-03 0.1196651 at 100iterations 1.5166781E-03 6.0302734E-02 at 110iterations 6.9893256E-04 2.4826050E-02 at 120iterations finished qdiffx linear iterations at : 11:37:20 total time elapsed so far: 7.100000 # loops : 120 mean,max change (kT/e) : 6.9893256E-04 2.4826050E-02 energy calculations done at 7.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.270000 DelPhi exited at 11:37:20 7.276u 0.235s 0:07.78 96.4% 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 11:37:20 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2032 !!! WARNING: HIR 430 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.840023 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): -6.098000 38.88100 ymin,ymax (A): 5.456000 61.86400 zmin,zma (A): -15.46600 29.33400 x,y,z range (A): 44.97900 56.40800 44.80000 scale (grids/A): 2.840023 object centre (A): 16.39150 33.66000 6.934000 number of atom coordinates read : 2032 total number of charged atoms : 1894 net assigned charge : 1.4007375E-02 assigned positive charge : 291.7658 centred at (gu) : 87.27290 102.2425 97.91438 assigned negative charge : -291.7523 centred at (gu) : 88.14044 101.9489 97.56892 start vw surface at 0.1200000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 138220 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19937 grid for indexing accessible points = 1.400000 m= 66180 mr = 95567 m= 24581 mr = 51646 m= 6364 mr = 19107 m= 919 mr = 4644 m= 50 mr = 539 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.6300001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.100000 number of dielectric boundary points 64800 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.230000 number of grid points assigned charge 15151 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) : 1.893348 object centre at (A) : 16.39150 33.66000 6.934000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2879885E-02 9.2620499E-02 midg,1,midg; midg,igrid,midg 5.3403463E-02 0.2537199 1,midg,midg; igrid,midg,midg 6.6168144E-02 -0.1704929 gauss-seidel spectral radius is 0.9992436 estimated iterations to convergence 287 setup time was (sec) 1.400000 now iterating at: 11:37:22 rms-change max change #iterations 8.618297 354.3923 at 10iterations 5.069813 127.4864 at 20iterations 2.957516 70.55693 at 30iterations 1.713286 41.16839 at 40iterations 0.9914474 21.18278 at 50iterations 0.5700665 11.28604 at 60iterations 0.3276139 7.261633 at 70iterations 0.1883308 3.997840 at 80iterations 0.1075508 2.219215 at 90iterations 6.1635841E-02 1.232803 at 100iterations 3.5313427E-02 0.7114449 at 110iterations 2.0097695E-02 0.3933296 at 120iterations 1.1501990E-02 0.2453108 at 130iterations 6.5761874E-03 0.1500702 at 140iterations 3.7651602E-03 7.2711945E-02 at 150iterations 2.1460375E-03 4.3582916E-02 at 160iterations 1.2262728E-03 2.5646806E-02 at 170iterations 6.9972820E-04 1.3973892E-02 at 180iterations finished qdiffx linear iterations at : 11:37:32 total time elapsed so far: 11.65000 # loops : 180 mean,max change (kT/e) : 6.9972820E-04 1.3973892E-02 energy calculations done at 11.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.81000 DelPhi exited at 11:37:33 11.813u 0.246s 0:12.33 97.7% 0+0k 0+0io 0pf+0w