Sat Oct 8 16:35:49 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 Sat Oct 8 2011 at 16:35:49 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: 373 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4631 !!! WARNING: GLM 204 has a net charge of -0.0940 !!! WARNING: FAD 994 has a net charge of -2.0000 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: 0.5453765 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): 16.99300 78.78500 ymin,ymax (A): 120.0730 185.3490 zmin,zma (A): -1.955000 59.50300 x,y,z range (A): 61.79200 65.27600 61.45800 scale (grids/A): 0.5453765 object centre (A): 47.88900 152.7110 28.77400 number of atom coordinates read : 4631 total number of charged atoms : 4419 net assigned charge : 2.906036 assigned positive charge : 706.5717 centred at (gu) : 91.61436 89.17049 87.26499 assigned negative charge : -703.6689 centred at (gu) : 91.57847 89.08591 87.27962 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 8774 nv = 96 ne = 84 npr = 94045 no. pairs analyzed = 94045 no. exposed pairs = 5467 no. arc points = 38430 no. surface atoms = 1831 nbur = 2800 mkacc time = 0.2000000 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 = 1.568000 m= 393 mr = 4804 m= 2 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 25 time to turn everything in is 0.4200000 number of dielectric boundary points 4345 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3771 ## 464 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 11541 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.3269257E-10 1.4373486E-11 midg,1,midg; midg,igrid,midg -8.6024643E-10 8.2995977E-10 1,midg,midg; igrid,midg,midg -1.2754478E-10 7.9979956E-10 gauss-seidel spectral radius is 0.9827871 estimated iterations to convergence 63 setup time was (sec) 0.6300000 now iterating at: 16:35:50 rms-change max change #iterations 9.3080088E-02 14.15186 at 10iterations 6.6308915E-03 0.8266764 at 20iterations 6.3338876E-04 8.0394268E-02 at 30iterations 1.4449336E-04 2.1257162E-02 at 40iterations 4.3667107E-05 6.5453053E-03 at 50iterations finished qdiffx linear iterations at : 16:35:52 total time elapsed so far: 3.050000 # loops : 50 mean,max change (kT/e) : 4.3667107E-05 6.5453053E-03 energy calculations done at 3.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.220000 DelPhi exited at 16:35:53 3.226u 0.149s 0:03.68 91.3% 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 Sat Oct 8 2011 at 16:35:53 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: 373 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4631 !!! WARNING: GLM 204 has a net charge of -0.0940 !!! WARNING: FAD 994 has a net charge of -2.0000 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: 1.636130 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): 16.99300 78.78500 ymin,ymax (A): 120.0730 185.3490 zmin,zma (A): -1.955000 59.50300 x,y,z range (A): 61.79200 65.27600 61.45800 scale (grids/A): 1.636130 object centre (A): 47.88900 152.7110 28.77400 number of atom coordinates read : 4631 total number of charged atoms : 4419 net assigned charge : 2.906036 assigned positive charge : 706.5717 centred at (gu) : 94.84193 87.51068 81.79389 assigned negative charge : -703.6689 centred at (gu) : 94.73531 87.25739 81.83868 start vw surface at 0.1900000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 99074 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38430 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 30723 mr = 69755 m= 3509 mr = 21512 m= 103 mr = 1935 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 1551 time to turn everything in is 0.6400000 number of dielectric boundary points 40200 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 435 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 33805 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) : 0.5453765 object centre at (A) : 47.88900 152.7110 28.77400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5529758E-03 8.7392116E-03 midg,1,midg; midg,igrid,midg 1.4344411E-02 3.4568813E-02 1,midg,midg; igrid,midg,midg -1.0679465E-02 -1.6030191E-02 gauss-seidel spectral radius is 0.9983457 estimated iterations to convergence 195 setup time was (sec) 0.9100000 now iterating at: 16:35:54 rms-change max change #iterations 4.376111 252.7626 at 10iterations 1.893643 85.83511 at 20iterations 0.8218346 33.49970 at 30iterations 0.3564501 12.11562 at 40iterations 0.1547564 4.696927 at 50iterations 6.7331217E-02 1.929544 at 60iterations 2.9281991E-02 0.9743938 at 70iterations 1.2743107E-02 0.3851955 at 80iterations 5.5501983E-03 0.1643333 at 90iterations 2.4241686E-03 7.3204041E-02 at 100iterations 1.0641740E-03 3.0732155E-02 at 110iterations 4.7139093E-04 1.3801575E-02 at 120iterations finished qdiffx linear iterations at : 16:36:00 total time elapsed so far: 6.990000 # loops : 120 mean,max change (kT/e) : 4.7139093E-04 1.3801575E-02 energy calculations done at 6.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.160000 DelPhi exited at 16:36:00 7.166u 0.151s 0:07.72 94.6% 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 Sat Oct 8 2011 at 16:36:00 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: 373 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4631 !!! WARNING: GLM 204 has a net charge of -0.0940 !!! WARNING: FAD 994 has a net charge of -2.0000 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: 2.454195 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): 16.99300 78.78500 ymin,ymax (A): 120.0730 185.3490 zmin,zma (A): -1.955000 59.50300 x,y,z range (A): 61.79200 65.27600 61.45800 scale (grids/A): 2.454195 object centre (A): 47.88900 152.7110 28.77400 number of atom coordinates read : 4631 total number of charged atoms : 4419 net assigned charge : 2.906036 assigned positive charge : 706.5717 centred at (gu) : 97.26265 86.26577 77.69044 assigned negative charge : -703.6689 centred at (gu) : 97.10282 85.88612 77.75799 start vw surface at 0.1800000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 230582 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38430 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 106835 mr = 170436 m= 31101 mr = 85544 m= 5829 mr = 23699 m= 517 mr = 4123 m= 12 mr = 285 m= 0 mr = 2 time to grow re-entrant surface = 0.9299999 no. cavity mid-points inaccessible to solvent = 5050 time to turn everything in is 1.590000 number of dielectric boundary points 90787 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 34 iepsmp to db, and charging done at 1.720000 number of grid points assigned charge 35312 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) : 1.636130 object centre at (A) : 47.88900 152.7110 28.77400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.7610449E-03 0.1836322 midg,1,midg; midg,igrid,midg 0.2207902 0.6251481 1,midg,midg; igrid,midg,midg -0.1495034 -0.2331607 gauss-seidel spectral radius is 0.9992161 estimated iterations to convergence 282 setup time was (sec) 1.870000 now iterating at: 16:36:02 rms-change max change #iterations 11.16039 461.1326 at 10iterations 6.440928 204.4028 at 20iterations 3.692757 125.2942 at 30iterations 2.114863 97.16360 at 40iterations 1.207714 38.18363 at 50iterations 0.6883226 15.61488 at 60iterations 0.3909324 9.291078 at 70iterations 0.2212830 4.054056 at 80iterations 0.1256274 2.136539 at 90iterations 7.1484491E-02 1.248244 at 100iterations 4.0360581E-02 0.6898670 at 110iterations 2.2883955E-02 0.3993168 at 120iterations 1.2937050E-02 0.2408295 at 130iterations 7.3332619E-03 0.1250992 at 140iterations 4.1442080E-03 7.5595856E-02 at 150iterations 2.3481706E-03 3.7398338E-02 at 160iterations 1.3283943E-03 2.4733543E-02 at 170iterations 7.5207534E-04 1.2351990E-02 at 180iterations finished qdiffx linear iterations at : 16:36:12 total time elapsed so far: 11.61000 # loops : 180 mean,max change (kT/e) : 7.5207534E-04 1.2351990E-02 energy calculations done at 11.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.79000 DelPhi exited at 16:36:13 11.792u 0.163s 0:12.25 97.5% 0+0k 0+0io 0pf+0w