Sat Oct 8 16:06:16 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 16:06:16 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2332 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: GLM 711 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6538349 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): -2.409000 45.62100 ymin,ymax (A): -16.93400 29.38100 zmin,zma (A): -17.37000 37.07800 x,y,z range (A): 48.03000 46.31500 54.44800 scale (grids/A): 0.6538349 object centre (A): 21.60600 6.223500 9.853999 number of atom coordinates read : 2332 total number of charged atoms : 2269 net assigned charge : 4.806003 assigned positive charge : 349.3510 centred at (gu) : 90.68584 88.92036 90.19148 assigned negative charge : -344.5458 centred at (gu) : 90.68093 89.06567 90.20004 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6821 nv = 96 ne = 84 npr = 46162 no. pairs analyzed = 46162 no. exposed pairs = 3068 no. arc points = 20978 no. surface atoms = 1038 nbur = 1294 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 388 mr = 3727 m= 0 mr = 52 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3430 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1981 ## 168 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 8089 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0906983E-08 9.1221288E-09 midg,1,midg; midg,igrid,midg 3.9544474E-08 -9.4479349E-09 1,midg,midg; igrid,midg,midg 8.1277935E-09 1.2413746E-08 gauss-seidel spectral radius is 0.9878570 estimated iterations to convergence 74 setup time was (sec) 0.6200000 now iterating at: 16:06:17 rms-change max change #iterations 0.1523101 26.08047 at 10iterations 1.5516452E-02 2.363590 at 20iterations 1.6544323E-03 0.2098694 at 30iterations 2.0345552E-04 2.4936676E-02 at 40iterations 3.6356611E-05 5.4893494E-03 at 50iterations finished qdiffx linear iterations at : 16:06:20 total time elapsed so far: 4.060000 # loops : 50 mean,max change (kT/e) : 3.6356611E-05 5.4893494E-03 energy calculations done at 4.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.240000 DelPhi exited at 16:06:21 4.247u 0.250s 0:04.78 93.9% 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 16:06:21 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2332 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: GLM 711 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.961505 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): -2.409000 45.62100 ymin,ymax (A): -16.93400 29.38100 zmin,zma (A): -17.37000 37.07800 x,y,z range (A): 48.03000 46.31500 54.44800 scale (grids/A): 1.961505 object centre (A): 21.60600 6.223500 9.853999 number of atom coordinates read : 2332 total number of charged atoms : 2269 net assigned charge : 4.806003 assigned positive charge : 349.3510 centred at (gu) : 92.05714 86.76060 90.57378 assigned negative charge : -344.5458 centred at (gu) : 92.04250 87.19693 90.60006 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 72843 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20978 grid for indexing accessible points = 1.400000 m= 26972 mr = 50208 m= 4775 mr = 19786 m= 324 mr = 3164 m= 2 mr = 147 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 300 time to turn everything in is 0.5900000 number of dielectric boundary points 31611 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 119 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 17900 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) : 0.6538349 object centre at (A) : 21.60600 6.223500 9.853999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3635661E-02 2.0364093E-02 midg,1,midg; midg,igrid,midg 3.0936077E-02 -5.2071949E-03 1,midg,midg; igrid,midg,midg 1.0021895E-03 -3.7136786E-02 gauss-seidel spectral radius is 0.9986889 estimated iterations to convergence 219 setup time was (sec) 0.9400000 now iterating at: 16:06:22 rms-change max change #iterations 4.252640 174.0302 at 10iterations 2.022473 64.24069 at 20iterations 0.9618445 32.78080 at 30iterations 0.4590995 15.23564 at 40iterations 0.2180169 6.666659 at 50iterations 0.1040505 3.718078 at 60iterations 4.9431935E-02 1.802121 at 70iterations 2.3496475E-02 0.7202358 at 80iterations 1.1193317E-02 0.3440237 at 90iterations 5.3645461E-03 0.1708594 at 100iterations 2.5591161E-03 7.7140808E-02 at 110iterations 1.2248677E-03 3.7210464E-02 at 120iterations finished qdiffx linear iterations at : 16:06:31 total time elapsed so far: 9.510000 # loops : 120 mean,max change (kT/e) : 1.2248677E-03 3.7210464E-02 energy calculations done at 9.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.690000 DelPhi exited at 16:06:31 9.694u 0.256s 0:10.23 97.1% 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 16:06:31 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2332 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: GLM 711 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.942257 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): -2.409000 45.62100 ymin,ymax (A): -16.93400 29.38100 zmin,zma (A): -17.37000 37.07800 x,y,z range (A): 48.03000 46.31500 54.44800 scale (grids/A): 2.942257 object centre (A): 21.60600 6.223500 9.853999 number of atom coordinates read : 2332 total number of charged atoms : 2269 net assigned charge : 4.806003 assigned positive charge : 349.3510 centred at (gu) : 93.08558 85.14092 90.86053 assigned negative charge : -344.5458 centred at (gu) : 93.06365 85.79536 90.90016 start vw surface at 0.1500000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 168471 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20978 grid for indexing accessible points = 1.400000 m= 85505 mr = 121812 m= 32922 mr = 69500 m= 8856 mr = 26678 m= 1432 mr = 6900 m= 117 mr = 1010 m= 1 mr = 63 m= 0 mr = 0 time to grow re-entrant surface = 0.8600001 no. cavity mid-points inaccessible to solvent = 1008 time to turn everything in is 1.460000 number of dielectric boundary points 71341 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.610000 number of grid points assigned charge 18152 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) : 1.961505 object centre at (A) : 21.60600 6.223500 9.853999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2305645 0.2108788 midg,1,midg; midg,igrid,midg 0.2335904 -7.9272635E-02 1,midg,midg; igrid,midg,midg 4.3966718E-02 -0.5847937 gauss-seidel spectral radius is 0.9992740 estimated iterations to convergence 293 setup time was (sec) 1.820000 now iterating at: 16:06:33 rms-change max change #iterations 9.860272 476.1335 at 10iterations 5.799812 123.3348 at 20iterations 3.402051 65.25578 at 30iterations 1.986570 39.29348 at 40iterations 1.162488 23.79608 at 50iterations 0.6776811 12.46536 at 60iterations 0.3931552 7.114441 at 70iterations 0.2285569 4.504952 at 80iterations 0.1329845 2.412157 at 90iterations 7.7009834E-02 1.489477 at 100iterations 4.4641603E-02 0.8148019 at 110iterations 2.5852149E-02 0.5020370 at 120iterations 1.4967610E-02 0.3015347 at 130iterations 8.6545032E-03 0.1550980 at 140iterations 5.0229449E-03 9.3799591E-02 at 150iterations 2.9133912E-03 5.9424877E-02 at 160iterations 1.6936354E-03 3.1040192E-02 at 170iterations 9.8866969E-04 1.8005371E-02 at 180iterations finished qdiffx linear iterations at : 16:06:47 total time elapsed so far: 15.33000 # loops : 180 mean,max change (kT/e) : 9.8866969E-04 1.8005371E-02 energy calculations done at 15.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.52000 DelPhi exited at 16:06:47 15.521u 0.250s 0:16.08 98.0% 0+0k 0+0io 0pf+0w