Mon Oct 10 14:06:22 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 14:06:22 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3039 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5625879 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): -3.346000 59.93300 ymin,ymax (A): -12.42600 34.17900 zmin,zma (A): 18.70800 71.07401 x,y,z range (A): 63.27900 46.60500 52.36600 scale (grids/A): 0.5625879 object centre (A): 28.29350 10.87650 44.89100 number of atom coordinates read : 3039 total number of charged atoms : 2894 net assigned charge : 10.50003 assigned positive charge : 467.0082 centred at (gu) : 90.73693 89.93022 89.00185 assigned negative charge : -456.5093 centred at (gu) : 90.81671 89.97928 88.99261 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6405 nv = 96 ne = 84 npr = 60003 no. pairs analyzed = 60003 no. exposed pairs = 3787 no. arc points = 26736 no. surface atoms = 1264 nbur = 1775 mkacc time = 0.1500000 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 = 1.512000 m= 270 mr = 3406 m= 0 mr = 11 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3258 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2629 ## 289 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8105 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4166380E-09 1.0716182E-09 midg,1,midg; midg,igrid,midg 1.8753645E-09 6.1312100E-10 1,midg,midg; igrid,midg,midg 1.8645485E-09 2.6756930E-10 gauss-seidel spectral radius is 0.9837068 estimated iterations to convergence 64 setup time was (sec) 0.6200000 now iterating at: 14:06:23 rms-change max change #iterations 8.7464429E-02 13.47678 at 10iterations 6.4531961E-03 1.126570 at 20iterations 7.9555274E-04 0.1098366 at 30iterations 3.1515601E-04 4.7555923E-02 at 40iterations 1.5694243E-04 2.3645401E-02 at 50iterations finished qdiffx linear iterations at : 14:06:27 total time elapsed so far: 4.810000 # loops : 50 mean,max change (kT/e) : 1.5694243E-04 2.3645401E-02 energy calculations done at 4.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.970000 DelPhi exited at 14:06:28 4.975u 0.402s 0:05.74 93.5% 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 14:06:28 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3039 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.687764 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): -3.346000 59.93300 ymin,ymax (A): -12.42600 34.17900 zmin,zma (A): 18.70800 71.07401 x,y,z range (A): 63.27900 46.60500 52.36600 scale (grids/A): 1.687764 object centre (A): 28.29350 10.87650 44.89100 number of atom coordinates read : 3039 total number of charged atoms : 2894 net assigned charge : 10.50003 assigned positive charge : 467.0082 centred at (gu) : 92.20994 89.78995 87.00507 assigned negative charge : -456.5093 centred at (gu) : 92.44958 89.93734 86.97784 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 70636 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26736 grid for indexing accessible points = 1.400000 m= 23763 mr = 48960 m= 2729 mr = 16619 m= 77 mr = 1371 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 166 time to turn everything in is 0.5900000 number of dielectric boundary points 30247 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 254 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 22317 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) : 0.5625879 object centre at (A) : 28.29350 10.87650 44.89100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1825630E-02 8.1177149E-03 midg,1,midg; midg,igrid,midg 8.7250546E-03 1.6164405E-03 1,midg,midg; igrid,midg,midg 2.3052508E-02 6.8507111E-03 gauss-seidel spectral radius is 0.9983131 estimated iterations to convergence 193 setup time was (sec) 0.9400000 now iterating at: 14:06:29 rms-change max change #iterations 3.652857 175.3619 at 10iterations 1.572177 69.91140 at 20iterations 0.6765563 26.46741 at 30iterations 0.2902245 10.34413 at 40iterations 0.1255655 4.333610 at 50iterations 5.3938564E-02 1.811371 at 60iterations 2.3315307E-02 0.8984585 at 70iterations 1.0082994E-02 0.3563299 at 80iterations 4.4017606E-03 0.1475697 at 90iterations 1.9608489E-03 7.8029633E-02 at 100iterations 9.3244069E-04 3.4515381E-02 at 110iterations 5.0147570E-04 1.7671585E-02 at 120iterations finished qdiffx linear iterations at : 14:06:40 total time elapsed so far: 11.64000 # loops : 120 mean,max change (kT/e) : 5.0147570E-04 1.7671585E-02 energy calculations done at 11.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.81000 DelPhi exited at 14:06:41 11.813u 0.413s 0:12.92 94.5% 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 14:06:41 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3039 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.531646 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): -3.346000 59.93300 ymin,ymax (A): -12.42600 34.17900 zmin,zma (A): 18.70800 71.07401 x,y,z range (A): 63.27900 46.60500 52.36600 scale (grids/A): 2.531646 object centre (A): 28.29350 10.87650 44.89100 number of atom coordinates read : 3039 total number of charged atoms : 2894 net assigned charge : 10.50003 assigned positive charge : 467.0082 centred at (gu) : 93.31464 89.68480 85.50719 assigned negative charge : -456.5093 centred at (gu) : 93.67427 89.90578 85.46661 start vw surface at 0.1300000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 164147 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26736 grid for indexing accessible points = 1.400000 m= 80236 mr = 119571 m= 24967 mr = 64156 m= 4472 mr = 18941 m= 395 mr = 2980 m= 7 mr = 192 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 623 time to turn everything in is 1.450000 number of dielectric boundary points 68385 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.580000 number of grid points assigned charge 23138 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) : 1.687764 object centre at (A) : 28.29350 10.87650 44.89100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3777296 0.1082353 midg,1,midg; midg,igrid,midg 0.1160154 -2.0226238E-02 1,midg,midg; igrid,midg,midg 0.3562804 -7.8061678E-02 gauss-seidel spectral radius is 0.9991807 estimated iterations to convergence 276 setup time was (sec) 1.780000 now iterating at: 14:06:43 rms-change max change #iterations 9.300441 278.1434 at 10iterations 5.338551 140.7779 at 20iterations 3.042240 80.94544 at 30iterations 1.729140 38.54380 at 40iterations 0.9782451 23.04221 at 50iterations 0.5524524 11.88942 at 60iterations 0.3106991 6.827885 at 70iterations 0.1751088 3.567482 at 80iterations 9.8262861E-02 2.006476 at 90iterations 5.5134077E-02 1.061339 at 100iterations 3.1056004E-02 0.6572323 at 110iterations 1.7391462E-02 0.3469524 at 120iterations 9.7706495E-03 0.2076797 at 130iterations 5.4920041E-03 0.1233416 at 140iterations 3.1056625E-03 7.6073647E-02 at 150iterations 1.7782679E-03 3.9924622E-02 at 160iterations 1.0431316E-03 2.3507595E-02 at 170iterations 6.4237451E-04 1.5379906E-02 at 180iterations finished qdiffx linear iterations at : 14:07:01 total time elapsed so far: 19.36000 # loops : 180 mean,max change (kT/e) : 6.4237451E-04 1.5379906E-02 energy calculations done at 19.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.52000 DelPhi exited at 14:07:01 19.529u 0.458s 0:20.40 97.8% 0+0k 0+0io 0pf+0w