Mon Oct 10 17:07:17 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 17:07:17 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3689 !!! WARNING: HEM 900 has a net charge of 1.4000 !!! WARNING: ZN9 951 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5575131 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): -30.01000 33.84500 ymin,ymax (A): -31.51900 31.33500 zmin,zma (A): 29.12400 86.44600 x,y,z range (A): 63.85500 62.85400 57.32200 scale (grids/A): 0.5575131 object centre (A): 1.917500 -9.2000008E-02 57.78500 number of atom coordinates read : 3689 total number of charged atoms : 3495 net assigned charge : 5.800036 assigned positive charge : 554.4607 centred at (gu) : 89.99953 91.68898 91.21896 assigned negative charge : -548.6625 centred at (gu) : 90.12637 91.71004 91.22411 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7340 nv = 96 ne = 84 npr = 75521 no. pairs analyzed = 75521 no. exposed pairs = 4760 no. arc points = 33159 no. surface atoms = 1585 nbur = 2104 mkacc time = 0.1600000 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 = 1.540000 m= 288 mr = 3728 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3875 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3333 ## 376 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9565 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.7317744E-10 6.6915862E-10 midg,1,midg; midg,igrid,midg 5.5490490E-10 4.4513748E-10 1,midg,midg; igrid,midg,midg 2.1209283E-09 -1.0377856E-09 gauss-seidel spectral radius is 0.9834586 estimated iterations to convergence 64 setup time was (sec) 0.5700000 now iterating at: 17:07:18 rms-change max change #iterations 9.0739176E-02 12.33163 at 10iterations 6.6392906E-03 0.9922276 at 20iterations 6.5462256E-04 9.1670990E-02 at 30iterations 1.3237518E-04 2.1432877E-02 at 40iterations 3.5319226E-05 5.7849884E-03 at 50iterations finished qdiffx linear iterations at : 17:07:21 total time elapsed so far: 2.990000 # loops : 50 mean,max change (kT/e) : 3.5319226E-05 5.7849884E-03 energy calculations done at 2.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.170000 DelPhi exited at 17:07:21 3.176u 0.132s 0:03.99 82.7% 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 17:07:21 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3689 !!! WARNING: HEM 900 has a net charge of 1.4000 !!! WARNING: ZN9 951 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.672539 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): -30.01000 33.84500 ymin,ymax (A): -31.51900 31.33500 zmin,zma (A): 29.12400 86.44600 x,y,z range (A): 63.85500 62.85400 57.32200 scale (grids/A): 1.672539 object centre (A): 1.917500 -9.2000008E-02 57.78500 number of atom coordinates read : 3689 total number of charged atoms : 3495 net assigned charge : 5.800036 assigned positive charge : 554.4607 centred at (gu) : 89.99731 95.06597 93.65588 assigned negative charge : -548.6625 centred at (gu) : 90.37877 95.12948 93.67184 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 80704 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33159 grid for indexing accessible points = 1.400000 m= 24946 mr = 54599 m= 2714 mr = 16869 m= 86 mr = 1323 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 20 time to turn everything in is 0.5500000 number of dielectric boundary points 35656 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 355 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 26893 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) : 0.5575131 object centre at (A) : 1.917500 -9.2000008E-02 57.78500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.0112581E-03 4.9008192E-03 midg,1,midg; midg,igrid,midg -3.4999372E-03 2.1733016E-04 1,midg,midg; igrid,midg,midg 2.2892972E-02 -5.0772964E-03 gauss-seidel spectral radius is 0.9983407 estimated iterations to convergence 195 setup time was (sec) 0.8100000 now iterating at: 17:07:22 rms-change max change #iterations 3.950308 158.7487 at 10iterations 1.707979 59.06635 at 20iterations 0.7387965 24.84248 at 30iterations 0.3193191 10.47622 at 40iterations 0.1380531 4.733768 at 50iterations 5.9889935E-02 2.028683 at 60iterations 2.6012834E-02 0.8282995 at 70iterations 1.1292554E-02 0.3478007 at 80iterations 4.9184645E-03 0.1534500 at 90iterations 2.1739921E-03 7.5828552E-02 at 100iterations 9.7330631E-04 3.4339905E-02 at 110iterations 4.4828907E-04 1.4961243E-02 at 120iterations finished qdiffx linear iterations at : 17:07:28 total time elapsed so far: 6.720000 # loops : 120 mean,max change (kT/e) : 4.4828907E-04 1.4961243E-02 energy calculations done at 6.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.890000 DelPhi exited at 17:07:29 6.893u 0.187s 0:07.43 95.1% 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 17:07:29 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3689 !!! WARNING: HEM 900 has a net charge of 1.4000 !!! WARNING: ZN9 951 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.508809 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): -30.01000 33.84500 ymin,ymax (A): -31.51900 31.33500 zmin,zma (A): 29.12400 86.44600 x,y,z range (A): 63.85500 62.85400 57.32200 scale (grids/A): 2.508809 object centre (A): 1.917500 -9.2000008E-02 57.78500 number of atom coordinates read : 3689 total number of charged atoms : 3495 net assigned charge : 5.800036 assigned positive charge : 554.4607 centred at (gu) : 89.99577 97.59882 95.48343 assigned negative charge : -548.6625 centred at (gu) : 90.56821 97.69413 95.50761 start vw surface at 0.1800000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 187508 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33159 grid for indexing accessible points = 1.400000 m= 85913 mr = 133604 m= 24303 mr = 67319 m= 4200 mr = 17932 m= 380 mr = 2769 m= 4 mr = 177 m= 0 mr = 0 time to grow re-entrant surface = 0.7500001 no. cavity mid-points inaccessible to solvent = 87 time to turn everything in is 1.340000 number of dielectric boundary points 80507 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 25 iepsmp to db, and charging done at 1.470000 number of grid points assigned charge 27935 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) : 1.672539 object centre at (A) : 1.917500 -9.2000008E-02 57.78500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8662475E-02 0.1094817 midg,1,midg; midg,igrid,midg -0.2760393 4.2466346E-02 1,midg,midg; igrid,midg,midg 0.2932085 1.6586889E-02 gauss-seidel spectral radius is 0.9991990 estimated iterations to convergence 279 setup time was (sec) 1.620000 now iterating at: 17:07:31 rms-change max change #iterations 10.06938 359.6407 at 10iterations 5.786358 133.5680 at 20iterations 3.302138 80.35075 at 30iterations 1.880343 40.64010 at 40iterations 1.069533 21.38380 at 50iterations 0.6060616 14.11445 at 60iterations 0.3421721 7.224713 at 70iterations 0.1933075 4.240229 at 80iterations 0.1092292 2.052269 at 90iterations 6.1571561E-02 1.272129 at 100iterations 3.4649760E-02 0.7553787 at 110iterations 1.9543553E-02 0.3844538 at 120iterations 1.1003996E-02 0.2003632 at 130iterations 6.2024854E-03 0.1305656 at 140iterations 3.5012139E-03 7.6663971E-02 at 150iterations 1.9875597E-03 4.0071487E-02 at 160iterations 1.1337799E-03 2.3550034E-02 at 170iterations 6.5475615E-04 1.3809204E-02 at 180iterations finished qdiffx linear iterations at : 17:07:40 total time elapsed so far: 11.19000 # loops : 180 mean,max change (kT/e) : 6.5475615E-04 1.3809204E-02 energy calculations done at 11.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.36000 DelPhi exited at 17:07:41 11.366u 0.202s 0:11.91 97.0% 0+0k 0+0io 0pf+0w