Mon Oct 10 14:00:46 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 Mon Oct 10 2011 at 14:00:46 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2589 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 475 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6287420 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): -31.91200 17.48800 ymin,ymax (A): -24.01900 23.00700 zmin,zma (A): -12.36000 44.26100 x,y,z range (A): 49.40000 47.02600 56.62100 scale (grids/A): 0.6287420 object centre (A): -7.212000 -0.5059996 15.95050 number of atom coordinates read : 2589 total number of charged atoms : 2457 net assigned charge : 4.000009 assigned positive charge : 393.1971 centred at (gu) : 88.51550 89.27963 89.88818 assigned negative charge : -389.1976 centred at (gu) : 88.43212 89.32406 89.78917 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6765 nv = 96 ne = 84 npr = 53633 no. pairs analyzed = 53633 no. exposed pairs = 2998 no. arc points = 21738 no. surface atoms = 1009 nbur = 1580 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 376 mr = 3846 m= 3 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 31 time to turn everything in is 0.2800000 number of dielectric boundary points 3239 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2127 ## 221 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8270 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.3711634E-09 1.2342252E-08 midg,1,midg; midg,igrid,midg 9.4215293E-09 4.3615606E-10 1,midg,midg; igrid,midg,midg -4.1433443E-09 8.2353715E-09 gauss-seidel spectral radius is 0.9868938 estimated iterations to convergence 71 setup time was (sec) 0.5100000 now iterating at: 14:00:47 rms-change max change #iterations 0.1367115 20.83323 at 10iterations 1.2997782E-02 1.945777 at 20iterations 1.2620441E-03 0.1981506 at 30iterations 1.1882573E-04 1.5291214E-02 at 40iterations 1.1466614E-05 1.5659332E-03 at 50iterations finished qdiffx linear iterations at : 14:00:49 total time elapsed so far: 3.020000 # loops : 50 mean,max change (kT/e) : 1.1466614E-05 1.5659332E-03 energy calculations done at 3.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.200000 DelPhi exited at 14:00:50 3.201u 0.171s 0:04.13 81.5% 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 Mon Oct 10 2011 at 14:00:50 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2589 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 475 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: 1.886226 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): -31.91200 17.48800 ymin,ymax (A): -24.01900 23.00700 zmin,zma (A): -12.36000 44.26100 x,y,z range (A): 49.40000 47.02600 56.62100 scale (grids/A): 1.886226 object centre (A): -7.212000 -0.5059996 15.95050 number of atom coordinates read : 2589 total number of charged atoms : 2457 net assigned charge : 4.000009 assigned positive charge : 393.1971 centred at (gu) : 85.54606 87.83861 89.66391 assigned negative charge : -389.1976 centred at (gu) : 85.29612 87.97188 89.36737 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 73453 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21738 grid for indexing accessible points = 1.400000 m= 26361 mr = 51554 m= 4154 mr = 19877 m= 252 mr = 2694 m= 6 mr = 106 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 4173 time to turn everything in is 0.5100000 number of dielectric boundary points 29995 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 160 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 19316 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) : 0.6287420 object centre at (A) : -7.212000 -0.5059996 15.95050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8085377E-02 2.2186907E-02 midg,1,midg; midg,igrid,midg 1.2469419E-02 1.9853280E-03 1,midg,midg; igrid,midg,midg -1.3580037E-03 2.9702937E-02 gauss-seidel spectral radius is 0.9986060 estimated iterations to convergence 212 setup time was (sec) 0.7900000 now iterating at: 14:00:51 rms-change max change #iterations 4.146572 171.1440 at 10iterations 1.933041 77.83030 at 20iterations 0.8977464 30.23260 at 30iterations 0.4166080 13.41761 at 40iterations 0.1939592 6.051289 at 50iterations 9.0004727E-02 2.793709 at 60iterations 4.1714773E-02 1.340149 at 70iterations 1.9432424E-02 0.7274590 at 80iterations 9.0419855E-03 0.2995794 at 90iterations 4.1840593E-03 0.1270256 at 100iterations 1.9531159E-03 6.5292358E-02 at 110iterations 9.0940058E-04 2.7950287E-02 at 120iterations finished qdiffx linear iterations at : 14:00:58 total time elapsed so far: 7.120000 # loops : 120 mean,max change (kT/e) : 9.0940058E-04 2.7950287E-02 energy calculations done at 7.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.290000 DelPhi exited at 14:01:00 7.293u 0.196s 0:10.06 74.3% 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 Mon Oct 10 2011 at 14:01:02 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2589 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 475 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: 2.829339 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): -31.91200 17.48800 ymin,ymax (A): -24.01900 23.00700 zmin,zma (A): -12.36000 44.26100 x,y,z range (A): 49.40000 47.02600 56.62100 scale (grids/A): 2.829339 object centre (A): -7.212000 -0.5059996 15.95050 number of atom coordinates read : 2589 total number of charged atoms : 2457 net assigned charge : 4.000009 assigned positive charge : 393.1971 centred at (gu) : 83.31898 86.75763 89.49582 assigned negative charge : -389.1976 centred at (gu) : 82.94424 86.95774 89.05090 start vw surface at 0.1800000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 169528 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21738 grid for indexing accessible points = 1.400000 m= 86649 mr = 124379 m= 31006 mr = 72070 m= 7413 mr = 25201 m= 1069 mr = 5724 m= 83 mr = 732 m= 1 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 13962 time to turn everything in is 1.320000 number of dielectric boundary points 67594 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.460000 number of grid points assigned charge 19652 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) : 1.886226 object centre at (A) : -7.212000 -0.5059996 15.95050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1525499 0.2078655 midg,1,midg; midg,igrid,midg 0.1292518 2.1545602E-02 1,midg,midg; igrid,midg,midg -7.1670189E-03 0.3708149 gauss-seidel spectral radius is 0.9992444 estimated iterations to convergence 287 setup time was (sec) 1.620000 now iterating at: 14:01:04 rms-change max change #iterations 9.669569 302.6972 at 10iterations 5.566797 124.0338 at 20iterations 3.183657 58.34547 at 30iterations 1.821782 34.66917 at 40iterations 1.039353 18.28840 at 50iterations 0.5935657 12.25470 at 60iterations 0.3386293 6.611834 at 70iterations 0.1938553 3.648176 at 80iterations 0.1104604 2.025091 at 90iterations 6.3009277E-02 1.240654 at 100iterations 3.5979655E-02 0.6468658 at 110iterations 2.0506719E-02 0.3800049 at 120iterations 1.1703489E-02 0.2278423 at 130iterations 6.6844067E-03 0.1322660 at 140iterations 3.8094891E-03 6.7504883E-02 at 150iterations 2.1728424E-03 4.2549133E-02 at 160iterations 1.2392965E-03 2.3376465E-02 at 170iterations 7.0734980E-04 1.3656616E-02 at 180iterations finished qdiffx linear iterations at : 14:01:14 total time elapsed so far: 12.29000 # loops : 180 mean,max change (kT/e) : 7.0734980E-04 1.3656616E-02 energy calculations done at 12.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.46000 DelPhi exited at 14:01:15 12.467u 0.227s 0:13.32 95.1% 0+0k 0+0io 0pf+0w