Tue Oct 11 03:46:25 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 03:46:25 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2781 !!! WARNING: ASP 288 has a net charge of -0.7280 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6489245 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): 10.28800 65.14800 ymin,ymax (A): -5.425000 47.36700 zmin,zma (A): -6.785000 46.69000 x,y,z range (A): 54.86000 52.79200 53.47500 scale (grids/A): 0.6489245 object centre (A): 37.71800 20.97100 19.95250 number of atom coordinates read : 2781 total number of charged atoms : 2633 net assigned charge : 4.772015 assigned positive charge : 424.8588 centred at (gu) : 91.94612 90.24901 90.38815 assigned negative charge : -420.0873 centred at (gu) : 91.72601 90.43713 90.46431 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7790 nv = 96 ne = 84 npr = 56678 no. pairs analyzed = 56678 no. exposed pairs = 3413 no. arc points = 24039 no. surface atoms = 1146 nbur = 1635 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 457 mr = 4332 m= 2 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3844 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2429 ## 258 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 9371 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8839046E-08 -4.3128505E-09 midg,1,midg; midg,igrid,midg 3.5895273E-08 -2.3615343E-08 1,midg,midg; igrid,midg,midg -1.8147974E-08 6.5013715E-08 gauss-seidel spectral radius is 0.9877099 estimated iterations to convergence 74 setup time was (sec) 0.5900000 now iterating at: 03:46:26 rms-change max change #iterations 0.1627264 24.22790 at 10iterations 1.6790280E-02 2.457336 at 20iterations 1.8387910E-03 0.2394829 at 30iterations 2.4045211E-04 3.3128738E-02 at 40iterations 5.0467133E-05 6.9637299E-03 at 50iterations finished qdiffx linear iterations at : 03:46:28 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 5.0467133E-05 6.9637299E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 03:46:29 3.408u 0.186s 0:04.00 89.5% 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 03:46:29 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2781 !!! WARNING: ASP 288 has a net charge of -0.7280 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: 1.946774 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): 10.28800 65.14800 ymin,ymax (A): -5.425000 47.36700 zmin,zma (A): -6.785000 46.69000 x,y,z range (A): 54.86000 52.79200 53.47500 scale (grids/A): 1.946774 object centre (A): 37.71800 20.97100 19.95250 number of atom coordinates read : 2781 total number of charged atoms : 2633 net assigned charge : 4.772015 assigned positive charge : 424.8588 centred at (gu) : 95.83764 90.74641 91.16397 assigned negative charge : -420.0873 centred at (gu) : 95.17792 91.31115 91.39267 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 83699 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24039 grid for indexing accessible points = 1.400000 m= 31943 mr = 58230 m= 5342 mr = 23961 m= 404 mr = 3464 m= 4 mr = 161 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 598 time to turn everything in is 0.6700000 number of dielectric boundary points 35576 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 173 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 20792 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) : 0.6489245 object centre at (A) : 37.71800 20.97100 19.95250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3135832E-02 -2.5476720E-02 midg,1,midg; midg,igrid,midg 3.8106557E-02 -7.5095552E-03 1,midg,midg; igrid,midg,midg -8.0106454E-03 8.3073266E-02 gauss-seidel spectral radius is 0.9987108 estimated iterations to convergence 221 setup time was (sec) 0.9600000 now iterating at: 03:46:30 rms-change max change #iterations 4.630957 198.0308 at 10iterations 2.221266 74.98447 at 20iterations 1.065073 32.24749 at 30iterations 0.5094141 15.01850 at 40iterations 0.2436090 7.628283 at 50iterations 0.1165545 3.534762 at 60iterations 5.6056194E-02 1.701014 at 70iterations 2.6943699E-02 0.8575420 at 80iterations 1.2877419E-02 0.4075308 at 90iterations 6.1987350E-03 0.1778088 at 100iterations 2.9943874E-03 9.1415405E-02 at 110iterations 1.4434194E-03 4.3895721E-02 at 120iterations finished qdiffx linear iterations at : 03:46:37 total time elapsed so far: 7.490000 # loops : 120 mean,max change (kT/e) : 1.4434194E-03 4.3895721E-02 energy calculations done at 7.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.670000 DelPhi exited at 03:46:38 7.670u 0.201s 0:08.43 93.3% 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 Tue Oct 11 2011 at 03:46:38 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2781 !!! WARNING: ASP 288 has a net charge of -0.7280 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: 2.920160 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): 10.28800 65.14800 ymin,ymax (A): -5.425000 47.36700 zmin,zma (A): -6.785000 46.69000 x,y,z range (A): 54.86000 52.79200 53.47500 scale (grids/A): 2.920160 object centre (A): 37.71800 20.97100 19.95250 number of atom coordinates read : 2781 total number of charged atoms : 2633 net assigned charge : 4.772015 assigned positive charge : 424.8588 centred at (gu) : 98.75629 91.11958 91.74574 assigned negative charge : -420.0873 centred at (gu) : 97.76671 91.96653 92.08890 start vw surface at 0.1600000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 193151 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24039 grid for indexing accessible points = 1.400000 m= 101723 mr = 140685 m= 38804 mr = 83921 m= 9861 mr = 31633 m= 1632 mr = 7587 m= 121 mr = 1112 m= 0 mr = 57 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 1864 time to turn everything in is 1.640000 number of dielectric boundary points 80297 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.780000 number of grid points assigned charge 21062 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) : 1.946774 object centre at (A) : 37.71800 20.97100 19.95250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2166006 -0.3865015 midg,1,midg; midg,igrid,midg 0.4544936 4.9455225E-02 1,midg,midg; igrid,midg,midg -6.2889241E-02 0.7956215 gauss-seidel spectral radius is 0.9992837 estimated iterations to convergence 295 setup time was (sec) 1.950000 now iterating at: 03:46:40 rms-change max change #iterations 10.78420 561.1986 at 10iterations 6.368977 148.8667 at 20iterations 3.743476 70.84794 at 30iterations 2.195270 44.02106 at 40iterations 1.286360 26.16758 at 50iterations 0.7493153 14.07751 at 60iterations 0.4374430 7.612892 at 70iterations 0.2548941 4.632751 at 80iterations 0.1485503 2.424717 at 90iterations 8.6470455E-02 1.420467 at 100iterations 5.0312798E-02 0.9326286 at 110iterations 2.9323680E-02 0.5108109 at 120iterations 1.7042475E-02 0.2941360 at 130iterations 9.9693285E-03 0.1768112 at 140iterations 5.8126384E-03 9.5192909E-02 at 150iterations 3.4370741E-03 6.1948776E-02 at 160iterations 2.0435709E-03 3.7815094E-02 at 170iterations 1.2353170E-03 2.3895264E-02 at 180iterations finished qdiffx linear iterations at : 03:46:51 total time elapsed so far: 13.23000 # loops : 180 mean,max change (kT/e) : 1.2353170E-03 2.3895264E-02 energy calculations done at 13.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.40000 DelPhi exited at 03:46:52 13.406u 0.281s 0:14.47 94.5% 0+0k 0+0io 0pf+0w