Mon Oct 10 13:59:24 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 Mon Oct 10 2011 at 13:59:24 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 = 2125 !!! WARNING: ASL 51 has a net charge of -0.1000 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: 0.7233126 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): -14.68900 33.21600 ymin,ymax (A): -21.32800 26.85300 zmin,zma (A): -4.841000 44.37700 x,y,z range (A): 47.90500 48.18100 49.21800 scale (grids/A): 0.7233126 object centre (A): 9.263500 2.762500 19.76800 number of atom coordinates read : 2125 total number of charged atoms : 1985 net assigned charge : -7.099978 assigned positive charge : 321.1918 centred at (gu) : 89.15151 87.83202 88.01579 assigned negative charge : -328.2920 centred at (gu) : 89.17017 87.80961 88.24044 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7622 nv = 96 ne = 84 npr = 44077 no. pairs analyzed = 44077 no. exposed pairs = 2690 no. arc points = 19027 no. surface atoms = 907 nbur = 1218 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 486 mr = 4195 m= 5 mr = 82 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 66 time to turn everything in is 0.1800000 number of dielectric boundary points 3836 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1629 ## 130 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 8179 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0873990E-07 -1.7592659E-07 midg,1,midg; midg,igrid,midg -1.5840243E-07 -4.9156796E-08 1,midg,midg; igrid,midg,midg -8.7934161E-08 -8.7600128E-08 gauss-seidel spectral radius is 0.9900440 estimated iterations to convergence 82 setup time was (sec) 0.3600000 now iterating at: 13:59:25 rms-change max change #iterations 0.2291063 30.28801 at 10iterations 2.9208019E-02 3.590109 at 20iterations 3.8111734E-03 0.5231247 at 30iterations 4.8786044E-04 6.8664551E-02 at 40iterations 6.2833758E-05 8.2635880E-03 at 50iterations finished qdiffx linear iterations at : 13:59:28 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 6.2833758E-05 8.2635880E-03 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 13:59:28 3.363u 0.187s 0:03.87 91.4% 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 Mon Oct 10 2011 at 13:59:28 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 = 2125 !!! WARNING: ASL 51 has a net charge of -0.1000 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: 2.169938 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): -14.68900 33.21600 ymin,ymax (A): -21.32800 26.85300 zmin,zma (A): -4.841000 44.37700 x,y,z range (A): 47.90500 48.18100 49.21800 scale (grids/A): 2.169938 object centre (A): 9.263500 2.762500 19.76800 number of atom coordinates read : 2125 total number of charged atoms : 1985 net assigned charge : -7.099978 assigned positive charge : 321.1918 centred at (gu) : 87.45443 83.49580 84.04713 assigned negative charge : -328.2920 centred at (gu) : 87.51041 83.42885 84.72144 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 79989 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19027 grid for indexing accessible points = 1.400000 m= 31139 mr = 54806 m= 5905 mr = 23482 m= 540 mr = 3991 m= 13 mr = 292 m= 0 mr = 1 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 1945 time to turn everything in is 0.4000000 number of dielectric boundary points 35014 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 52 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 15780 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) : 0.7233126 object centre at (A) : 9.263500 2.762500 19.76800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.0204635E-02 -9.4978362E-02 midg,1,midg; midg,igrid,midg -2.2598334E-02 -1.2630004E-02 1,midg,midg; igrid,midg,midg -1.1645824E-02 -4.4722818E-02 gauss-seidel spectral radius is 0.9988821 estimated iterations to convergence 237 setup time was (sec) 0.6200000 now iterating at: 13:59:29 rms-change max change #iterations 4.979413 192.3945 at 10iterations 2.477543 86.47942 at 20iterations 1.247929 40.17129 at 30iterations 0.6245881 18.53986 at 40iterations 0.3151649 9.456473 at 50iterations 0.1582128 4.842953 at 60iterations 7.9597391E-02 2.415879 at 70iterations 3.9976411E-02 1.224304 at 80iterations 2.0154418E-02 0.6575212 at 90iterations 1.0126065E-02 0.2922363 at 100iterations 5.0947769E-03 0.1641579 at 110iterations 2.5653092E-03 7.8948975E-02 at 120iterations finished qdiffx linear iterations at : 13:59:36 total time elapsed so far: 7.680000 # loops : 120 mean,max change (kT/e) : 2.5653092E-03 7.8948975E-02 energy calculations done at 7.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.820000 DelPhi exited at 13:59:37 7.825u 0.200s 0:08.44 95.0% 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 Mon Oct 10 2011 at 13:59:37 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2125 !!! WARNING: ASL 51 has a net charge of -0.1000 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: 3.254907 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): -14.68900 33.21600 ymin,ymax (A): -21.32800 26.85300 zmin,zma (A): -4.841000 44.37700 x,y,z range (A): 47.90500 48.18100 49.21800 scale (grids/A): 3.254907 object centre (A): 9.263500 2.762500 19.76800 number of atom coordinates read : 2125 total number of charged atoms : 1985 net assigned charge : -7.099978 assigned positive charge : 321.1918 centred at (gu) : 86.18167 80.24366 81.07067 assigned negative charge : -328.2920 centred at (gu) : 86.26559 80.14327 82.08221 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 184437 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19027 grid for indexing accessible points = 1.400000 m= 96628 mr = 132319 m= 39467 mr = 79929 m= 11170 mr = 32384 m= 2352 mr = 8759 m= 234 mr = 1790 m= 8 mr = 144 m= 0 mr = 0 time to grow re-entrant surface = 0.6200000 no. cavity mid-points inaccessible to solvent = 6237 time to turn everything in is 1.250000 number of dielectric boundary points 78971 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 15880 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) : 2.169938 object centre at (A) : 9.263500 2.762500 19.76800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7186992 -0.8272862 midg,1,midg; midg,igrid,midg -0.1553041 -1.6149178E-02 1,midg,midg; igrid,midg,midg -0.1094132 -0.5495318 gauss-seidel spectral radius is 0.9993176 estimated iterations to convergence 302 setup time was (sec) 1.510000 now iterating at: 13:59:38 rms-change max change #iterations 10.89869 362.4799 at 10iterations 6.423007 125.1648 at 20iterations 3.777931 65.29088 at 30iterations 2.223219 37.71602 at 40iterations 1.307023 22.59649 at 50iterations 0.7686068 12.80672 at 60iterations 0.4508759 8.488411 at 70iterations 0.2649415 4.323442 at 80iterations 0.1549249 2.729365 at 90iterations 9.1131039E-02 1.486444 at 100iterations 5.3465318E-02 0.8854551 at 110iterations 3.1393129E-02 0.5064015 at 120iterations 1.8416483E-02 0.3233948 at 130iterations 1.0802529E-02 0.1882906 at 140iterations 6.3429368E-03 0.1198206 at 150iterations 3.7143980E-03 6.1756134E-02 at 160iterations 2.1849838E-03 3.8253784E-02 at 170iterations 1.2819793E-03 2.4225235E-02 at 180iterations finished qdiffx linear iterations at : 13:59:50 total time elapsed so far: 12.95000 # loops : 180 mean,max change (kT/e) : 1.2819793E-03 2.4225235E-02 energy calculations done at 12.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.07000 DelPhi exited at 13:59:50 13.077u 0.223s 0:13.70 97.0% 0+0k 0+0io 0pf+0w