Tue Nov 22 14:16:50 PST 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 Tue Nov 22 2011 at 14:16:54 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 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: 0.5945125 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): -35.33000 9.940000 ymin,ymax (A): 1.485000 41.15500 zmin,zma (A): -1.884000 57.99700 x,y,z range (A): 45.27000 39.67000 59.88100 scale (grids/A): 0.5945125 object centre (A): -12.69500 21.32000 28.05650 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 290.5000 centred at (gu) : 90.51721 89.48878 89.79864 assigned negative charge : -287.5003 centred at (gu) : 90.44737 89.60838 89.78966 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 4676 nv = 96 ne = 84 npr = 40478 no. pairs analyzed = 40478 no. exposed pairs = 2459 no. arc points = 17073 no. surface atoms = 835 nbur = 1135 mkacc time = 6.0000002E-02 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 = 1.456000 m= 206 mr = 2543 m= 0 mr = 27 time to grow re-entrant surface = 7.0000008E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1500000 number of dielectric boundary points 2312 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1779 ## 199 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 5750 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.8437402E-10 1.2002846E-09 midg,1,midg; midg,igrid,midg 4.2049857E-09 -1.5137395E-09 1,midg,midg; igrid,midg,midg -4.8423482E-10 2.9596843E-09 gauss-seidel spectral radius is 0.9853063 estimated iterations to convergence 68 setup time was (sec) 0.3600000 now iterating at: 14:16:57 rms-change max change #iterations 8.6605832E-02 15.61512 at 10iterations 7.1408520E-03 1.355766 at 20iterations 5.8606488E-04 9.6584320E-02 at 30iterations 4.8249902E-05 7.9383850E-03 at 40iterations 3.9000656E-06 8.4877014E-04 at 50iterations finished qdiffx linear iterations at : 14:17:07 total time elapsed so far: 3.640000 # loops : 50 mean,max change (kT/e) : 3.9000656E-06 8.4877014E-04 energy calculations done at 3.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.770000 DelPhi exited at 14:17:10 3.772u 0.231s 0:16.46 24.3% 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 Tue Nov 22 2011 at 14:17:14 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 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: 1.783537 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): -35.33000 9.940000 ymin,ymax (A): 1.485000 41.15500 zmin,zma (A): -1.884000 57.99700 x,y,z range (A): 45.27000 39.67000 59.88100 scale (grids/A): 1.783537 object centre (A): -12.69500 21.32000 28.05650 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 290.5000 centred at (gu) : 91.55171 88.46632 89.39601 assigned negative charge : -287.5003 centred at (gu) : 91.34240 88.82534 89.36917 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 50371 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17073 grid for indexing accessible points = 1.400000 m= 17884 mr = 34342 m= 2375 mr = 13467 m= 89 mr = 1472 m= 0 mr = 27 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 442 time to turn everything in is 0.2600000 number of dielectric boundary points 21411 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 172 iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 14299 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) : 0.5945125 object centre at (A) : -12.69500 21.32000 28.05650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8425051E-02 2.2064732E-02 midg,1,midg; midg,igrid,midg 1.8263416E-03 -6.9950731E-03 1,midg,midg; igrid,midg,midg -1.3268217E-03 -1.1688876E-03 gauss-seidel spectral radius is 0.9983675 estimated iterations to convergence 196 setup time was (sec) 0.5300000 now iterating at: 14:17:19 rms-change max change #iterations 3.129619 139.0818 at 10iterations 1.364429 61.13649 at 20iterations 0.5987549 23.62372 at 30iterations 0.2592213 9.735398 at 40iterations 0.1128216 4.818747 at 50iterations 4.9257163E-02 1.835865 at 60iterations 2.1424375E-02 0.8565445 at 70iterations 9.3374196E-03 0.3999939 at 80iterations 4.0883212E-03 0.1503677 at 90iterations 1.7852023E-03 6.8565369E-02 at 100iterations 7.7840686E-04 2.8766155E-02 at 110iterations 3.3847051E-04 1.3641357E-02 at 120iterations finished qdiffx linear iterations at : 14:17:43 total time elapsed so far: 8.650000 # loops : 120 mean,max change (kT/e) : 3.3847051E-04 1.3641357E-02 energy calculations done at 8.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.780000 DelPhi exited at 14:17:45 8.784u 0.259s 0:31.71 28.4% 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 Tue Nov 22 2011 at 14:17:48 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 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: 2.675306 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): -35.33000 9.940000 ymin,ymax (A): 1.485000 41.15500 zmin,zma (A): -1.884000 57.99700 x,y,z range (A): 45.27000 39.67000 59.88100 scale (grids/A): 2.675306 object centre (A): -12.69500 21.32000 28.05650 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 290.5000 centred at (gu) : 92.32748 87.69949 89.09392 assigned negative charge : -287.5003 centred at (gu) : 92.01355 88.23812 89.05380 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 116421 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17073 grid for indexing accessible points = 1.400000 m= 58727 mr = 83230 m= 20290 mr = 48385 m= 4109 mr = 16673 m= 485 mr = 3095 m= 13 mr = 341 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 1561 time to turn everything in is 0.7200000 number of dielectric boundary points 48321 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 14703 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) : 1.783537 object centre at (A) : -12.69500 21.32000 28.05650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2735916 0.1400524 midg,1,midg; midg,igrid,midg -1.5041990E-02 -9.9019229E-02 1,midg,midg; igrid,midg,midg -4.0732007E-02 -5.8541127E-02 gauss-seidel spectral radius is 0.9991616 estimated iterations to convergence 273 setup time was (sec) 1.010000 now iterating at: 14:17:54 rms-change max change #iterations 7.601635 323.9226 at 10iterations 4.255246 120.2601 at 20iterations 2.385705 56.68385 at 30iterations 1.326926 29.12476 at 40iterations 0.7365464 16.17885 at 50iterations 0.4097347 9.063119 at 60iterations 0.2269064 5.822021 at 70iterations 0.1257455 2.632754 at 80iterations 6.9536522E-02 1.449871 at 90iterations 3.8444515E-02 0.8317490 at 100iterations 2.1353526E-02 0.4800949 at 110iterations 1.1801580E-02 0.2556305 at 120iterations 6.5222471E-03 0.1468172 at 130iterations 3.6087129E-03 8.8476181E-02 at 140iterations 1.9959444E-03 4.7391891E-02 at 150iterations 1.1073361E-03 2.7833939E-02 at 160iterations 6.0980930E-04 1.2925148E-02 at 170iterations 3.3747984E-04 7.4992180E-03 at 180iterations finished qdiffx linear iterations at : 14:18:32 total time elapsed so far: 13.44000 # loops : 180 mean,max change (kT/e) : 3.3747984E-04 7.4992180E-03 energy calculations done at 13.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.56000 DelPhi exited at 14:18:35 13.565u 0.298s 0:47.69 29.0% 0+0k 0+0io 0pf+0w