Tue Oct 11 07:39:45 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 Tue Oct 11 2011 at 07:39:45 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2734 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6342645 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): -13.16100 42.96700 ymin,ymax (A): -21.65700 26.43900 zmin,zma (A): -5.804000 40.11700 x,y,z range (A): 56.12800 48.09600 45.92100 scale (grids/A): 0.6342645 object centre (A): 14.90300 2.390999 17.15650 number of atom coordinates read : 2734 total number of charged atoms : 2373 net assigned charge : 8.500014 assigned positive charge : 379.5231 centred at (gu) : 89.85137 88.31831 89.23774 assigned negative charge : -371.0237 centred at (gu) : 89.85955 88.26382 89.42108 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6613 nv = 96 ne = 84 npr = 51461 no. pairs analyzed = 51461 no. exposed pairs = 2905 no. arc points = 20232 no. surface atoms = 993 nbur = 1741 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 348 mr = 3787 m= 1 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3134 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1975 ## 195 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7943 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.2394475E-08 -6.1379017E-09 midg,1,midg; midg,igrid,midg 7.2615434E-09 1.0925018E-08 1,midg,midg; igrid,midg,midg 1.1538576E-08 9.3408223E-09 gauss-seidel spectral radius is 0.9871082 estimated iterations to convergence 72 setup time was (sec) 0.5000000 now iterating at: 07:39:46 rms-change max change #iterations 0.1332984 22.18580 at 10iterations 1.3287911E-02 1.826007 at 20iterations 1.3921954E-03 0.2100544 at 30iterations 1.6414191E-04 2.5535583E-02 at 40iterations 2.3228184E-05 3.3874512E-03 at 50iterations finished qdiffx linear iterations at : 07:39:48 total time elapsed so far: 2.890000 # loops : 50 mean,max change (kT/e) : 2.3228184E-05 3.3874512E-03 energy calculations done at 2.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.070000 DelPhi exited at 07:39:49 3.075u 0.134s 0:03.80 84.2% 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 Oct 11 2011 at 07:39:49 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2734 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.902794 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): -13.16100 42.96700 ymin,ymax (A): -21.65700 26.43900 zmin,zma (A): -5.804000 40.11700 x,y,z range (A): 56.12800 48.09600 45.92100 scale (grids/A): 1.902794 object centre (A): 14.90300 2.390999 17.15650 number of atom coordinates read : 2734 total number of charged atoms : 2373 net assigned charge : 8.500014 assigned positive charge : 379.5231 centred at (gu) : 89.55360 84.95479 87.71303 assigned negative charge : -371.0237 centred at (gu) : 89.57833 84.79127 88.26302 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 71553 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20232 grid for indexing accessible points = 1.400000 m= 25996 mr = 50698 m= 3966 mr = 19596 m= 203 mr = 2456 m= 4 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 426 time to turn everything in is 0.5300000 number of dielectric boundary points 28900 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 151 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 18593 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) : 0.6342645 object centre at (A) : 14.90300 2.390999 17.15650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5697086E-02 -5.1588882E-03 midg,1,midg; midg,igrid,midg 7.3961867E-03 2.2008784E-02 1,midg,midg; igrid,midg,midg 2.0738289E-02 2.5921633E-02 gauss-seidel spectral radius is 0.9986128 estimated iterations to convergence 213 setup time was (sec) 0.7900000 now iterating at: 07:39:50 rms-change max change #iterations 4.073330 156.6122 at 10iterations 1.898659 65.46829 at 20iterations 0.8884326 33.10369 at 30iterations 0.4146810 13.37140 at 40iterations 0.1934746 5.723245 at 50iterations 9.0379335E-02 3.034956 at 60iterations 4.2054232E-02 1.386435 at 70iterations 1.9628711E-02 0.6294689 at 80iterations 9.1691846E-03 0.3095627 at 90iterations 4.2867702E-03 0.1348152 at 100iterations 2.0080300E-03 7.1792603E-02 at 110iterations 9.3987666E-04 3.2104492E-02 at 120iterations finished qdiffx linear iterations at : 07:39:56 total time elapsed so far: 6.660000 # loops : 120 mean,max change (kT/e) : 9.3987666E-04 3.2104492E-02 energy calculations done at 6.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.820000 DelPhi exited at 07:39:57 6.826u 0.170s 0:07.50 93.2% 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 Oct 11 2011 at 07:39:57 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2734 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.854191 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): -13.16100 42.96700 ymin,ymax (A): -21.65700 26.43900 zmin,zma (A): -5.804000 40.11700 x,y,z range (A): 56.12800 48.09600 45.92100 scale (grids/A): 2.854191 object centre (A): 14.90300 2.390999 17.15650 number of atom coordinates read : 2734 total number of charged atoms : 2373 net assigned charge : 8.500014 assigned positive charge : 379.5231 centred at (gu) : 89.33038 82.43203 86.56946 assigned negative charge : -371.0237 centred at (gu) : 89.36767 82.18687 87.39452 start vw surface at 0.1800000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 165596 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20232 grid for indexing accessible points = 1.400000 m= 84969 mr = 122702 m= 30238 mr = 70698 m= 6959 mr = 24368 m= 1001 mr = 5248 m= 45 mr = 673 m= 2 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 1272 time to turn everything in is 1.270000 number of dielectric boundary points 65116 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.390000 number of grid points assigned charge 18982 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) : 1.902794 object centre at (A) : 14.90300 2.390999 17.15650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4488740 -0.1150420 midg,1,midg; midg,igrid,midg 4.5636833E-02 0.2266996 1,midg,midg; igrid,midg,midg 0.1113736 0.1802887 gauss-seidel spectral radius is 0.9992396 estimated iterations to convergence 286 setup time was (sec) 1.540000 now iterating at: 07:39:58 rms-change max change #iterations 9.529432 398.1992 at 10iterations 5.474170 112.3769 at 20iterations 3.135532 60.19287 at 30iterations 1.795843 36.49651 at 40iterations 1.025161 19.07753 at 50iterations 0.5849319 10.35869 at 60iterations 0.3343125 5.774008 at 70iterations 0.1907206 3.534227 at 80iterations 0.1086934 2.034773 at 90iterations 6.2227730E-02 1.092731 at 100iterations 3.5501752E-02 0.6515694 at 110iterations 2.0252019E-02 0.3907852 at 120iterations 1.1578100E-02 0.2320576 at 130iterations 6.6298121E-03 0.1317901 at 140iterations 3.8146088E-03 7.0064545E-02 at 150iterations 2.2144858E-03 4.0660858E-02 at 160iterations 1.2977967E-03 2.4303436E-02 at 170iterations 7.7365927E-04 1.4228821E-02 at 180iterations finished qdiffx linear iterations at : 07:40:08 total time elapsed so far: 11.17000 # loops : 180 mean,max change (kT/e) : 7.7365927E-04 1.4228821E-02 energy calculations done at 11.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.35000 DelPhi exited at 07:40:09 11.356u 0.184s 0:11.82 97.5% 0+0k 0+0io 0pf+0w