Tue Oct 11 03:27:00 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 03:27:00 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 = 2558 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: 0.5931949 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): -16.00200 38.46200 ymin,ymax (A): 6.685000 55.39000 zmin,zma (A): 5.664000 65.67800 x,y,z range (A): 54.46400 48.70500 60.01400 scale (grids/A): 0.5931949 object centre (A): 11.23000 31.03750 35.67100 number of atom coordinates read : 2558 total number of charged atoms : 2409 net assigned charge : 8.8512897E-06 assigned positive charge : 384.7718 centred at (gu) : 89.11125 90.11092 90.26775 assigned negative charge : -384.7726 centred at (gu) : 89.05416 90.04372 90.36248 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6119 nv = 96 ne = 84 npr = 49348 no. pairs analyzed = 49348 no. exposed pairs = 3525 no. arc points = 25713 no. surface atoms = 1180 nbur = 1378 mkacc time = 7.9999998E-02 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 = 1.456000 m= 285 mr = 3021 m= 0 mr = 20 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 35 time to turn everything in is 0.1800000 number of dielectric boundary points 3363 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2606 ## 297 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 7602 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.5949618E-09 -2.9529290E-09 midg,1,midg; midg,igrid,midg -1.9038595E-09 2.0248290E-09 1,midg,midg; igrid,midg,midg -2.0385258E-09 1.3681097E-09 gauss-seidel spectral radius is 0.9853028 estimated iterations to convergence 68 setup time was (sec) 0.3700000 now iterating at: 03:27:01 rms-change max change #iterations 9.9004038E-02 18.41908 at 10iterations 8.2014399E-03 1.279185 at 20iterations 7.4698433E-04 0.1230698 at 30iterations 1.2515562E-04 2.6952744E-02 at 40iterations 3.7305028E-05 8.7451935E-03 at 50iterations finished qdiffx linear iterations at : 03:27:03 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 3.7305028E-05 8.7451935E-03 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 03:27:04 3.369u 0.208s 0:04.26 83.5% 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 03:27:04 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 = 2558 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: 1.779585 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): -16.00200 38.46200 ymin,ymax (A): 6.685000 55.39000 zmin,zma (A): 5.664000 65.67800 x,y,z range (A): 54.46400 48.70500 60.01400 scale (grids/A): 1.779585 object centre (A): 11.23000 31.03750 35.67100 number of atom coordinates read : 2558 total number of charged atoms : 2409 net assigned charge : 8.8512897E-06 assigned positive charge : 384.7718 centred at (gu) : 87.33315 90.33213 90.80255 assigned negative charge : -384.7726 centred at (gu) : 87.16232 90.13096 91.08726 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 66764 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25713 grid for indexing accessible points = 1.400000 m= 21223 mr = 43771 m= 2504 mr = 14394 m= 92 mr = 1271 m= 0 mr = 25 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 527 time to turn everything in is 0.3200000 number of dielectric boundary points 31122 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 235 iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 18777 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) : 0.5931949 object centre at (A) : 11.23000 31.03750 35.67100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1716320E-02 -1.7089663E-02 midg,1,midg; midg,igrid,midg -1.4985315E-02 9.6666003E-03 1,midg,midg; igrid,midg,midg -8.5390331E-03 -2.6994443E-04 gauss-seidel spectral radius is 0.9984512 estimated iterations to convergence 202 setup time was (sec) 0.5300000 now iterating at: 03:27:05 rms-change max change #iterations 3.698799 167.9744 at 10iterations 1.636092 71.98018 at 20iterations 0.7274477 27.29203 at 30iterations 0.3230445 11.98655 at 40iterations 0.1435088 5.041369 at 50iterations 6.3966282E-02 2.301200 at 60iterations 2.8498968E-02 0.9740009 at 70iterations 1.2749395E-02 0.4706268 at 80iterations 5.6820386E-03 0.2011271 at 90iterations 2.5385662E-03 9.5188141E-02 at 100iterations 1.1405951E-03 4.1809082E-02 at 110iterations 5.2254112E-04 1.8286705E-02 at 120iterations finished qdiffx linear iterations at : 03:27:12 total time elapsed so far: 7.680000 # loops : 120 mean,max change (kT/e) : 5.2254112E-04 1.8286705E-02 energy calculations done at 7.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.820000 DelPhi exited at 03:27:13 7.819u 0.215s 0:08.34 96.1% 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 Tue Oct 11 2011 at 03:27:13 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 = 2558 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: 2.669377 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): -16.00200 38.46200 ymin,ymax (A): 6.685000 55.39000 zmin,zma (A): 5.664000 65.67800 x,y,z range (A): 54.46400 48.70500 60.01400 scale (grids/A): 2.669377 object centre (A): 11.23000 31.03750 35.67100 number of atom coordinates read : 2558 total number of charged atoms : 2409 net assigned charge : 8.8512897E-06 assigned positive charge : 384.7718 centred at (gu) : 85.99964 90.49811 91.20365 assigned negative charge : -384.7726 centred at (gu) : 85.74346 90.19643 91.63076 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 154533 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25713 grid for indexing accessible points = 1.400000 m= 71676 mr = 106856 m= 21783 mr = 56319 m= 4129 mr = 16193 m= 399 mr = 2745 m= 21 mr = 213 m= 0 mr = 4 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 1846 time to turn everything in is 0.8100000 number of dielectric boundary points 70211 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 19266 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) : 1.779585 object centre at (A) : 11.23000 31.03750 35.67100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1813270 -0.1505327 midg,1,midg; midg,igrid,midg -0.2345571 0.1361266 1,midg,midg; igrid,midg,midg -0.1316719 -2.6300345E-02 gauss-seidel spectral radius is 0.9992173 estimated iterations to convergence 282 setup time was (sec) 1.060000 now iterating at: 03:27:14 rms-change max change #iterations 9.214341 341.3872 at 10iterations 5.378901 171.4802 at 20iterations 3.107643 73.36475 at 30iterations 1.787284 40.63770 at 40iterations 1.023191 23.32829 at 50iterations 0.5848498 14.45777 at 60iterations 0.3331339 7.861432 at 70iterations 0.1899250 4.541187 at 80iterations 0.1076240 2.224877 at 90iterations 6.1142378E-02 1.319138 at 100iterations 3.4689821E-02 0.7321646 at 110iterations 1.9695191E-02 0.3835297 at 120iterations 1.1148809E-02 0.2234364 at 130iterations 6.3013844E-03 0.1267920 at 140iterations 3.5765332E-03 7.3500633E-02 at 150iterations 2.0232769E-03 4.2472839E-02 at 160iterations 1.1443479E-03 2.1543980E-02 at 170iterations 6.4707192E-04 1.2571812E-02 at 180iterations finished qdiffx linear iterations at : 03:27:26 total time elapsed so far: 12.87000 # loops : 180 mean,max change (kT/e) : 6.4707192E-04 1.2571812E-02 energy calculations done at 12.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.00000 DelPhi exited at 03:27:26 13.007u 0.247s 0:13.70 96.6% 0+0k 0+0io 0pf+0w