Tue Oct 11 07:08:01 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+sph.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 = amb.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 07:08:01 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3398 !!! WARNING: UMP 1145 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.4605910 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): -70.91700 5.995000 ymin,ymax (A): -83.91800 -30.35000 zmin,zma (A): -54.11900 23.17300 x,y,z range (A): 76.91200 53.56800 77.29200 scale (grids/A): 0.4605910 object centre (A): -32.46100 -57.13400 -15.47300 number of atom coordinates read : 3398 total number of charged atoms : 3193 net assigned charge : 1.900011 assigned positive charge : 505.0044 centred at (gu) : 84.89228 89.96651 96.29644 assigned negative charge : -503.1060 centred at (gu) : 84.77857 90.03246 96.35330 start vw surface at 0.2300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 4506 nv = 96 ne = 84 npr = 67032 no. pairs analyzed = 67032 no. exposed pairs = 4331 no. arc points = 30153 no. surface atoms = 1474 nbur = 1924 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.848000 m= 129 mr = 2240 m= 1 mr = 4 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 0.3900000 number of dielectric boundary points 2392 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2640 ## 515 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 6011 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1050206E-12 -3.5785451E-11 midg,1,midg; midg,igrid,midg 1.3821617E-11 -6.4369252E-12 1,midg,midg; igrid,midg,midg -6.6346387E-11 4.8995343E-12 gauss-seidel spectral radius is 0.9758389 estimated iterations to convergence 53 setup time was (sec) 0.6200000 now iterating at: 07:08:02 rms-change max change #iterations 3.2273497E-02 6.720043 at 10iterations 2.3492386E-03 0.4308872 at 20iterations 6.9610070E-04 0.1542363 at 30iterations 2.5889851E-04 5.8684826E-02 at 40iterations 9.7286560E-05 2.2214890E-02 at 50iterations finished qdiffx linear iterations at : 07:08:04 total time elapsed so far: 3.050000 # loops : 50 mean,max change (kT/e) : 9.7286560E-05 2.2214890E-02 energy calculations done at 3.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.230000 DelPhi exited at 07:08:05 3.234u 0.126s 0:03.79 88.3% 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 07:08:05 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3398 !!! WARNING: UMP 1145 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.381773 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): -70.91700 5.995000 ymin,ymax (A): -83.91800 -30.35000 zmin,zma (A): -54.11900 23.17300 x,y,z range (A): 76.91200 53.56800 77.29200 scale (grids/A): 1.381773 object centre (A): -32.46100 -57.13400 -15.47300 number of atom coordinates read : 3398 total number of charged atoms : 3193 net assigned charge : 1.900011 assigned positive charge : 505.0044 centred at (gu) : 74.67556 89.89871 108.8881 assigned negative charge : -503.1060 centred at (gu) : 74.33530 90.09700 109.0599 start vw surface at 0.2600000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 51261 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30153 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.708000 m= 14472 mr = 34083 m= 948 mr = 9855 m= 13 mr = 397 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 22359 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 492 ## 13 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 22998 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) : 0.4605910 object centre at (A) : -32.46100 -57.13400 -15.47300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6396410E-05 -2.3192097E-04 midg,1,midg; midg,igrid,midg 3.1538014E-03 7.9219427E-04 1,midg,midg; igrid,midg,midg 3.7847902E-03 -5.9226724E-05 gauss-seidel spectral radius is 0.9974005 estimated iterations to convergence 156 setup time was (sec) 0.7600000 now iterating at: 07:08:06 rms-change max change #iterations 2.367154 130.8234 at 10iterations 0.8272977 42.06973 at 20iterations 0.2906918 12.43272 at 30iterations 0.1026969 4.909021 at 40iterations 3.6161128E-02 1.503587 at 50iterations 1.3037968E-02 0.5826011 at 60iterations 5.0248322E-03 0.2151775 at 70iterations 2.2656566E-03 0.1107025 at 80iterations 1.3003881E-03 6.0600281E-02 at 90iterations 8.7764877E-04 4.1158676E-02 at 100iterations 6.2525936E-04 2.8385162E-02 at 110iterations 4.5150326E-04 2.0422459E-02 at 120iterations finished qdiffx linear iterations at : 07:08:12 total time elapsed so far: 6.670000 # loops : 120 mean,max change (kT/e) : 4.5150326E-04 2.0422459E-02 energy calculations done at 6.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.860000 DelPhi exited at 07:08:12 6.863u 0.177s 0:07.40 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 Tue Oct 11 2011 at 07:08:12 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3398 !!! WARNING: UMP 1145 has a net charge of -0.1000 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: 2.072659 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): -70.91700 5.995000 ymin,ymax (A): -83.91800 -30.35000 zmin,zma (A): -54.11900 23.17300 x,y,z range (A): 76.91200 53.56800 77.29200 scale (grids/A): 2.072659 object centre (A): -32.46100 -57.13400 -15.47300 number of atom coordinates read : 3398 total number of charged atoms : 3193 net assigned charge : 1.900011 assigned positive charge : 505.0044 centred at (gu) : 67.01305 89.84767 118.3318 assigned negative charge : -503.1060 centred at (gu) : 66.50285 90.14529 118.5897 start vw surface at 0.1600000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 119449 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30153 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.708000 m= 52296 mr = 83763 m= 12474 mr = 40978 m= 1307 mr = 9379 m= 29 mr = 762 m= 0 mr = 0 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9200000 number of dielectric boundary points 50673 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 120 iepsmp to db, and charging done at 1.040000 number of grid points assigned charge 25321 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) : 1.381773 object centre at (A) : -32.46100 -57.13400 -15.47300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6330590E-03 0.1869497 midg,1,midg; midg,igrid,midg 6.0236812E-02 1.8560769E-02 1,midg,midg; igrid,midg,midg 8.4447101E-02 -2.0501821E-03 gauss-seidel spectral radius is 0.9988161 estimated iterations to convergence 230 setup time was (sec) 1.220000 now iterating at: 07:08:14 rms-change max change #iterations 6.832170 225.0681 at 10iterations 3.495621 112.7917 at 20iterations 1.772276 51.40900 at 30iterations 0.8936365 28.93378 at 40iterations 0.4490764 12.12899 at 50iterations 0.2247438 6.426180 at 60iterations 0.1125016 2.948254 at 70iterations 5.6132212E-02 1.374422 at 80iterations 2.8091589E-02 0.7244587 at 90iterations 1.4291139E-02 0.3757915 at 100iterations 7.4848603E-03 0.2095985 at 110iterations 4.1392241E-03 0.1211548 at 120iterations 2.5403539E-03 7.9648018E-02 at 130iterations 1.7479435E-03 4.9732208E-02 at 140iterations 1.3142185E-03 3.5882950E-02 at 150iterations 1.0355597E-03 2.6425600E-02 at 160iterations 8.3100726E-04 2.0919323E-02 at 170iterations 6.7217316E-04 1.6891479E-02 at 180iterations finished qdiffx linear iterations at : 07:08:24 total time elapsed so far: 11.49000 # loops : 180 mean,max change (kT/e) : 6.7217316E-04 1.6891479E-02 energy calculations done at 11.49000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.68000 DelPhi exited at 07:08:25 11.681u 0.269s 0:12.23 97.6% 0+0k 0+0io 0pf+0w