Mon Oct 10 11:09:25 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+sph.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 = amb.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 11:09:25 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: 230 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2119 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 0.7464877 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): -20.95200 24.22300 ymin,ymax (A): -8.012000 36.30200 zmin,zma (A): -3.471000 44.21900 x,y,z range (A): 45.17500 44.31400 47.69000 scale (grids/A): 0.7464877 object centre (A): 1.635500 14.14500 20.37400 number of atom coordinates read : 2119 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 317.0999 centred at (gu) : 89.00455 90.45747 90.18120 assigned negative charge : -323.3720 centred at (gu) : 89.02630 90.54695 90.37360 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 8131 nv = 96 ne = 84 npr = 43893 no. pairs analyzed = 43893 no. exposed pairs = 2677 no. arc points = 19128 no. surface atoms = 904 nbur = 1215 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 557 mr = 4510 m= 2 mr = 122 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.2600000 number of dielectric boundary points 4058 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1560 ## 140 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 8533 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.1457423E-08 -3.6733223E-07 midg,1,midg; midg,igrid,midg -2.1003045E-08 -2.5189181E-07 1,midg,midg; igrid,midg,midg -1.1990753E-07 -1.2667134E-07 gauss-seidel spectral radius is 0.9906487 estimated iterations to convergence 84 setup time was (sec) 0.5100000 now iterating at: 11:09:26 rms-change max change #iterations 0.2567287 40.00691 at 10iterations 3.4945238E-02 4.428914 at 20iterations 4.7749747E-03 0.6867218 at 30iterations 6.4336736E-04 8.0983162E-02 at 40iterations 9.0221380E-05 1.1251450E-02 at 50iterations finished qdiffx linear iterations at : 11:09:30 total time elapsed so far: 4.500000 # loops : 50 mean,max change (kT/e) : 9.0221380E-05 1.1251450E-02 energy calculations done at 4.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.650000 DelPhi exited at 11:09:31 4.656u 0.417s 0:05.33 94.9% 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 Mon Oct 10 2011 at 11:09:31 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: 230 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2119 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 2.239463 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): -20.95200 24.22300 ymin,ymax (A): -8.012000 36.30200 zmin,zma (A): -3.471000 44.21900 x,y,z range (A): 45.17500 44.31400 47.69000 scale (grids/A): 2.239463 object centre (A): 1.635500 14.14500 20.37400 number of atom coordinates read : 2119 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 317.0999 centred at (gu) : 87.01372 91.37245 90.54326 assigned negative charge : -323.3720 centred at (gu) : 87.07890 91.64087 91.12073 start vw surface at 0.1000000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 85459 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19128 grid for indexing accessible points = 1.400000 m= 34291 mr = 58985 m= 7422 mr = 26130 m= 852 mr = 5222 m= 26 mr = 485 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 57 time to turn everything in is 0.7200000 number of dielectric boundary points 37227 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 49 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 15766 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) : 0.7464877 object centre at (A) : 1.635500 14.14500 20.37400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4847872E-03 -0.1427921 midg,1,midg; midg,igrid,midg -2.5967970E-02 -3.8328782E-02 1,midg,midg; igrid,midg,midg 5.7043345E-04 -9.9932561E-03 gauss-seidel spectral radius is 0.9989423 estimated iterations to convergence 243 setup time was (sec) 1.030000 now iterating at: 11:09:32 rms-change max change #iterations 5.216746 204.7413 at 10iterations 2.661744 91.74435 at 20iterations 1.363052 37.64418 at 30iterations 0.6980748 18.93815 at 40iterations 0.3570434 9.501823 at 50iterations 0.1839320 5.516087 at 60iterations 9.3817577E-02 2.609719 at 70iterations 4.8077732E-02 1.316353 at 80iterations 2.4659447E-02 0.6811600 at 90iterations 1.2625962E-02 0.3641748 at 100iterations 6.4683533E-03 0.1679392 at 110iterations 3.3065029E-03 0.1136134 at 120iterations finished qdiffx linear iterations at : 11:09:43 total time elapsed so far: 11.72000 # loops : 120 mean,max change (kT/e) : 3.3065029E-03 0.1136134 energy calculations done at 11.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.90000 DelPhi exited at 11:09:43 11.902u 0.411s 0:12.60 97.6% 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 11:09:43 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: 230 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2119 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 3.359195 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): -20.95200 24.22300 ymin,ymax (A): -8.012000 36.30200 zmin,zma (A): -3.471000 44.21900 x,y,z range (A): 45.17500 44.31400 47.69000 scale (grids/A): 3.359195 object centre (A): 1.635500 14.14500 20.37400 number of atom coordinates read : 2119 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 317.0999 centred at (gu) : 85.52084 92.05865 90.81506 assigned negative charge : -323.3720 centred at (gu) : 85.61852 92.46130 91.68106 start vw surface at 0.1000000 fill in re-entrant regions at 0.9000000 boundary points on vw surface= 196835 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19128 grid for indexing accessible points = 1.400000 m= 105451 mr = 142328 m= 45067 mr = 87497 m= 14277 mr = 37298 m= 3404 mr = 11431 m= 498 mr = 2684 m= 22 mr = 338 m= 0 mr = 14 time to grow re-entrant surface = 1.200000 no. cavity mid-points inaccessible to solvent = 215 time to turn everything in is 2.230000 number of dielectric boundary points 83964 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.370000 number of grid points assigned charge 15824 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) : 2.239463 object centre at (A) : 1.635500 14.14500 20.37400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.9064503E-02 -1.280747 midg,1,midg; midg,igrid,midg -0.2387386 -0.1723114 1,midg,midg; igrid,midg,midg 7.6651148E-02 -0.1478762 gauss-seidel spectral radius is 0.9993241 estimated iterations to convergence 303 setup time was (sec) 2.580000 now iterating at: 11:09:46 rms-change max change #iterations 11.11003 275.9254 at 10iterations 6.564041 130.6617 at 20iterations 3.881902 65.70178 at 30iterations 2.286003 37.00262 at 40iterations 1.351625 24.53966 at 50iterations 0.7962798 14.30497 at 60iterations 0.4689879 7.175642 at 70iterations 0.2761623 4.681686 at 80iterations 0.1629359 2.748075 at 90iterations 9.5935144E-02 1.502371 at 100iterations 5.6485955E-02 0.8290014 at 110iterations 3.3170857E-02 0.4986601 at 120iterations 1.9503511E-02 0.3037033 at 130iterations 1.1496186E-02 0.1891509 at 140iterations 6.7725824E-03 0.1192317 at 150iterations 3.9850082E-03 6.0401917E-02 at 160iterations 2.3458155E-03 3.6193371E-02 at 170iterations 1.3794500E-03 2.0713806E-02 at 180iterations finished qdiffx linear iterations at : 11:10:04 total time elapsed so far: 20.24000 # loops : 180 mean,max change (kT/e) : 1.3794500E-03 2.0713806E-02 energy calculations done at 20.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.39000 DelPhi exited at 11:10:05 20.399u 0.491s 0:21.17 98.6% 0+0k 0+0io 0pf+0w