Tue Oct 11 05:59:31 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 Tue Oct 11 2011 at 05:59:31 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2065 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6718503 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): 2.665000 47.75400 ymin,ymax (A): -26.72300 12.33800 zmin,zma (A): -2.809000 50.17900 x,y,z range (A): 45.08900 39.06100 52.98800 scale (grids/A): 0.6718503 object centre (A): 25.20950 -7.192500 23.68500 number of atom coordinates read : 2065 total number of charged atoms : 1931 net assigned charge : 6.931010 assigned positive charge : 313.5771 centred at (gu) : 90.07112 90.28783 89.44024 assigned negative charge : -306.6461 centred at (gu) : 90.24708 90.26184 89.45641 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6215 nv = 96 ne = 84 npr = 41995 no. pairs analyzed = 41995 no. exposed pairs = 2499 no. arc points = 17155 no. surface atoms = 856 nbur = 1209 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 374 mr = 3505 m= 2 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3039 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1719 ## 175 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7215 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0830204E-08 1.8618149E-08 midg,1,midg; midg,igrid,midg 1.7671880E-08 3.1388225E-08 1,midg,midg; igrid,midg,midg 5.9701442E-08 -1.3816434E-08 gauss-seidel spectral radius is 0.9884610 estimated iterations to convergence 76 setup time was (sec) 0.3600000 now iterating at: 05:59:31 rms-change max change #iterations 0.1591762 27.06494 at 10iterations 1.7967658E-02 2.623924 at 20iterations 2.2561457E-03 0.3207951 at 30iterations 3.7391443E-04 5.1237106E-02 at 40iterations 8.7346460E-05 1.2405396E-02 at 50iterations finished qdiffx linear iterations at : 05:59:34 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 8.7346460E-05 1.2405396E-02 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 05:59:35 3.376u 0.159s 0:04.08 86.2% 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 05:59:35 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2065 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.015551 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): 2.665000 47.75400 ymin,ymax (A): -26.72300 12.33800 zmin,zma (A): -2.809000 50.17900 x,y,z range (A): 45.08900 39.06100 52.98800 scale (grids/A): 2.015551 object centre (A): 25.20950 -7.192500 23.68500 number of atom coordinates read : 2065 total number of charged atoms : 1931 net assigned charge : 6.931010 assigned positive charge : 313.5771 centred at (gu) : 90.21354 90.86344 88.32079 assigned negative charge : -306.6461 centred at (gu) : 90.74141 90.78573 88.36937 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 66986 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17155 grid for indexing accessible points = 1.400000 m= 25376 mr = 47313 m= 4169 mr = 18943 m= 283 mr = 2543 m= 3 mr = 111 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 27907 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 96 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 15279 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) : 0.6718503 object centre at (A) : 25.20950 -7.192500 23.68500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9649278E-02 5.0074026E-02 midg,1,midg; midg,igrid,midg 3.2183507E-03 1.9520102E-02 1,midg,midg; igrid,midg,midg 3.2003257E-02 4.0711821E-03 gauss-seidel spectral radius is 0.9987164 estimated iterations to convergence 221 setup time was (sec) 0.5500000 now iterating at: 05:59:36 rms-change max change #iterations 4.155654 230.0289 at 10iterations 1.996388 68.22362 at 20iterations 0.9574000 31.26849 at 30iterations 0.4607842 17.21675 at 40iterations 0.2212240 8.031008 at 50iterations 0.1064189 3.497546 at 60iterations 5.1210046E-02 1.733048 at 70iterations 2.4627997E-02 0.8019485 at 80iterations 1.1946811E-02 0.3921947 at 90iterations 5.8216942E-03 0.1777954 at 100iterations 2.8549912E-03 8.9031219E-02 at 110iterations 1.4378380E-03 4.8074722E-02 at 120iterations finished qdiffx linear iterations at : 05:59:43 total time elapsed so far: 7.600000 # loops : 120 mean,max change (kT/e) : 1.4378380E-03 4.8074722E-02 energy calculations done at 7.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.730000 DelPhi exited at 05:59:43 7.731u 0.216s 0:08.46 93.8% 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 05:59:43 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2065 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 3.023326 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): 2.665000 47.75400 ymin,ymax (A): -26.72300 12.33800 zmin,zma (A): -2.809000 50.17900 x,y,z range (A): 45.08900 39.06100 52.98800 scale (grids/A): 3.023326 object centre (A): 25.20950 -7.192500 23.68500 number of atom coordinates read : 2065 total number of charged atoms : 1931 net assigned charge : 6.931010 assigned positive charge : 313.5771 centred at (gu) : 90.32021 91.29517 87.48122 assigned negative charge : -306.6461 centred at (gu) : 91.11227 91.17850 87.55412 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 154613 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17155 grid for indexing accessible points = 1.400000 m= 81450 mr = 114130 m= 30232 mr = 67286 m= 7563 mr = 24330 m= 1181 mr = 5618 m= 68 mr = 800 m= 0 mr = 29 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9200000 number of dielectric boundary points 62914 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.000000 number of grid points assigned charge 15448 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) : 2.015551 object centre at (A) : 25.20950 -7.192500 23.68500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2975140 0.6598847 midg,1,midg; midg,igrid,midg 1.3677171E-02 0.1689073 1,midg,midg; igrid,midg,midg 0.2613626 6.9018878E-02 gauss-seidel spectral radius is 0.9992647 estimated iterations to convergence 291 setup time was (sec) 1.140000 now iterating at: 05:59:45 rms-change max change #iterations 9.566815 473.8596 at 10iterations 5.583583 149.3474 at 20iterations 3.257502 79.07497 at 30iterations 1.888106 44.78785 at 40iterations 1.099308 21.62600 at 50iterations 0.6373573 12.58938 at 60iterations 0.3706847 7.580597 at 70iterations 0.2141088 4.171501 at 80iterations 0.1237308 2.616419 at 90iterations 7.1772464E-02 1.342764 at 100iterations 4.1561820E-02 0.7499771 at 110iterations 2.4233336E-02 0.4727588 at 120iterations 1.4216423E-02 0.2863400 at 130iterations 8.4420517E-03 0.1636786 at 140iterations 5.1152408E-03 9.6620440E-02 at 150iterations 3.2154052E-03 6.6268921E-02 at 160iterations 2.1194946E-03 4.1328430E-02 at 170iterations 1.4771040E-03 2.6172638E-02 at 180iterations finished qdiffx linear iterations at : 05:59:56 total time elapsed so far: 12.30000 # loops : 180 mean,max change (kT/e) : 1.4771040E-03 2.6172638E-02 energy calculations done at 12.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.43000 DelPhi exited at 05:59:57 12.432u 0.239s 0:13.17 96.1% 0+0k 0+0io 0pf+0w