Sat Oct 8 11:36:48 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 11:36:48 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3363 !!! WARNING: HIZ 15 has a net charge of 0.2000 !!! WARNING: HIZ 17 has a net charge of 0.2000 !!! WARNING: HIZ 214 has a net charge of 0.2000 !!! WARNING: GLM 295 has a net charge of -0.6000 !!! WARNING: ZN4 472 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: 0.6368971 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): -23.36600 32.53000 ymin,ymax (A): -1.801000 51.28900 zmin,zma (A): 12.25600 60.06400 x,y,z range (A): 55.89600 53.09000 47.80800 scale (grids/A): 0.6368971 object centre (A): 4.582000 24.74400 36.16000 number of atom coordinates read : 3363 total number of charged atoms : 3216 net assigned charge : -1.599975 assigned positive charge : 511.9844 centred at (gu) : 90.72223 90.69972 89.15401 assigned negative charge : -513.5854 centred at (gu) : 90.78748 90.50217 89.30550 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8930 nv = 96 ne = 84 npr = 71575 no. pairs analyzed = 71575 no. exposed pairs = 3619 no. arc points = 24629 no. surface atoms = 1250 nbur = 2113 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 454 mr = 5487 m= 1 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 75 time to turn everything in is 0.3500000 number of dielectric boundary points 3826 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2408 ## 216 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 10901 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2536550E-08 -2.0174427E-08 midg,1,midg; midg,igrid,midg -2.6641569E-08 2.9140249E-08 1,midg,midg; igrid,midg,midg 5.7531628E-09 -1.3736653E-08 gauss-seidel spectral radius is 0.9872797 estimated iterations to convergence 72 setup time was (sec) 0.5800000 now iterating at: 11:36:49 rms-change max change #iterations 0.1688683 21.76228 at 10iterations 1.6953578E-02 2.191983 at 20iterations 1.6784843E-03 0.2025280 at 30iterations 1.6699953E-04 1.9251823E-02 at 40iterations 1.6656077E-05 2.3212433E-03 at 50iterations finished qdiffx linear iterations at : 11:36:52 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 1.6656077E-05 2.3212433E-03 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 11:36:52 3.360u 0.198s 0:03.90 91.0% 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 11:36:52 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3363 !!! WARNING: HIZ 15 has a net charge of 0.2000 !!! WARNING: HIZ 17 has a net charge of 0.2000 !!! WARNING: HIZ 214 has a net charge of 0.2000 !!! WARNING: GLM 295 has a net charge of -0.6000 !!! WARNING: ZN4 472 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.910691 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): -23.36600 32.53000 ymin,ymax (A): -1.801000 51.28900 zmin,zma (A): 12.25600 60.06400 x,y,z range (A): 55.89600 53.09000 47.80800 scale (grids/A): 1.910691 object centre (A): 4.582000 24.74400 36.16000 number of atom coordinates read : 3363 total number of charged atoms : 3216 net assigned charge : -1.599975 assigned positive charge : 511.9844 centred at (gu) : 92.16579 92.09816 87.46086 assigned negative charge : -513.5854 centred at (gu) : 92.36167 91.50610 87.91593 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 96639 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24629 grid for indexing accessible points = 1.400000 m= 37033 mr = 71332 m= 5914 mr = 29248 m= 339 mr = 4020 m= 5 mr = 122 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 2930 time to turn everything in is 0.6300000 number of dielectric boundary points 35208 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 145 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 25297 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) : 0.6368971 object centre at (A) : 4.582000 24.74400 36.16000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.5538827E-03 -5.4491635E-02 midg,1,midg; midg,igrid,midg -3.6797393E-02 3.6957186E-02 1,midg,midg; igrid,midg,midg 5.5150728E-04 -1.3176996E-02 gauss-seidel spectral radius is 0.9986967 estimated iterations to convergence 219 setup time was (sec) 0.9000000 now iterating at: 11:36:53 rms-change max change #iterations 5.000226 172.9893 at 10iterations 2.378788 69.70343 at 20iterations 1.133288 31.28111 at 30iterations 0.5392219 14.46603 at 40iterations 0.2581934 7.357113 at 50iterations 0.1234551 3.350476 at 60iterations 5.8983933E-02 1.584206 at 70iterations 2.8208753E-02 0.8325801 at 80iterations 1.3462734E-02 0.3736877 at 90iterations 6.4272569E-03 0.1919603 at 100iterations 3.0756320E-03 8.4327698E-02 at 110iterations 1.4698526E-03 4.1660309E-02 at 120iterations finished qdiffx linear iterations at : 11:36:59 total time elapsed so far: 6.960000 # loops : 120 mean,max change (kT/e) : 1.4698526E-03 4.1660309E-02 energy calculations done at 6.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.130000 DelPhi exited at 11:37:00 7.133u 0.161s 0:07.67 95.0% 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 11:37:00 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3363 !!! WARNING: HIZ 15 has a net charge of 0.2000 !!! WARNING: HIZ 17 has a net charge of 0.2000 !!! WARNING: HIZ 214 has a net charge of 0.2000 !!! WARNING: GLM 295 has a net charge of -0.6000 !!! WARNING: ZN4 472 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.866037 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): -23.36600 32.53000 ymin,ymax (A): -1.801000 51.28900 zmin,zma (A): 12.25600 60.06400 x,y,z range (A): 55.89600 53.09000 47.80800 scale (grids/A): 2.866037 object centre (A): 4.582000 24.74400 36.16000 number of atom coordinates read : 3363 total number of charged atoms : 3216 net assigned charge : -1.599975 assigned positive charge : 511.9844 centred at (gu) : 93.24841 93.14700 86.19096 assigned negative charge : -513.5854 centred at (gu) : 93.54227 92.25896 86.87366 start vw surface at 0.1700000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 223408 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24629 grid for indexing accessible points = 1.400000 m= 119462 mr = 171496 m= 45198 mr = 101793 m= 10821 mr = 38284 m= 1430 mr = 8492 m= 87 mr = 955 m= 2 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 10283 time to turn everything in is 1.650000 number of dielectric boundary points 79359 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.770000 number of grid points assigned charge 25726 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) : 1.910691 object centre at (A) : 4.582000 24.74400 36.16000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.7189913E-02 -0.6410199 midg,1,midg; midg,igrid,midg -0.3672161 0.3463908 1,midg,midg; igrid,midg,midg -0.1621357 -0.1322419 gauss-seidel spectral radius is 0.9992765 estimated iterations to convergence 293 setup time was (sec) 1.930000 now iterating at: 11:37:02 rms-change max change #iterations 11.53045 318.8221 at 10iterations 6.765073 126.8525 at 20iterations 3.954218 94.96484 at 30iterations 2.301556 49.55749 at 40iterations 1.338441 25.88577 at 50iterations 0.7805057 12.70551 at 60iterations 0.4523340 6.929315 at 70iterations 0.2625624 4.366034 at 80iterations 0.1522104 2.469415 at 90iterations 8.8081434E-02 1.322939 at 100iterations 5.1126130E-02 0.7921619 at 110iterations 2.9619252E-02 0.5208850 at 120iterations 1.7131891E-02 0.2810478 at 130iterations 9.9251326E-03 0.1517048 at 140iterations 5.7459180E-03 9.0591431E-02 at 150iterations 3.3254735E-03 5.0392151E-02 at 160iterations 1.9274749E-03 3.1387329E-02 at 170iterations 1.1152256E-03 1.8571258E-02 at 180iterations finished qdiffx linear iterations at : 11:37:12 total time elapsed so far: 11.53000 # loops : 180 mean,max change (kT/e) : 1.1152256E-03 1.8571258E-02 energy calculations done at 11.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.70000 DelPhi exited at 11:37:12 11.703u 0.163s 0:12.36 95.9% 0+0k 0+0io 0pf+0w