Tue Oct 11 06:19:28 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 06:19:28 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 = 2056 !!! WARNING: GLM 175 has a net charge of -0.0940 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 0.7248590 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): 18.11300 64.38500 ymin,ymax (A): -3.534000 33.21400 zmin,zma (A): 21.12100 70.23400 x,y,z range (A): 46.27200 36.74800 49.11300 scale (grids/A): 0.7248590 object centre (A): 41.24900 14.84000 45.67750 number of atom coordinates read : 2056 total number of charged atoms : 1921 net assigned charge : 5.931007 assigned positive charge : 312.1541 centred at (gu) : 90.04351 89.73424 89.24353 assigned negative charge : -306.2232 centred at (gu) : 90.20718 89.79438 89.26063 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7332 nv = 96 ne = 84 npr = 41247 no. pairs analyzed = 41247 no. exposed pairs = 2409 no. arc points = 16713 no. surface atoms = 820 nbur = 1236 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 508 mr = 4272 m= 4 mr = 119 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3453 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1549 ## 131 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 7975 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.9972276E-08 5.4602776E-08 midg,1,midg; midg,igrid,midg 1.2314138E-07 3.0452032E-08 1,midg,midg; igrid,midg,midg 1.8739632E-07 -4.3608122E-08 gauss-seidel spectral radius is 0.9900702 estimated iterations to convergence 82 setup time was (sec) 0.4800000 now iterating at: 06:19:29 rms-change max change #iterations 0.2227256 34.62217 at 10iterations 2.9016845E-02 4.582927 at 20iterations 4.0521035E-03 0.5316620 at 30iterations 6.6669029E-04 9.1528416E-02 at 40iterations 1.5678690E-04 2.1842957E-02 at 50iterations finished qdiffx linear iterations at : 06:19:32 total time elapsed so far: 3.080000 # loops : 50 mean,max change (kT/e) : 1.5678690E-04 2.1842957E-02 energy calculations done at 3.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.260000 DelPhi exited at 06:19:32 3.266u 0.190s 0:03.89 88.6% 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 06:19:32 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 = 2056 !!! WARNING: GLM 175 has a net charge of -0.0940 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 2.174577 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): 18.11300 64.38500 ymin,ymax (A): -3.534000 33.21400 zmin,zma (A): 21.12100 70.23400 x,y,z range (A): 46.27200 36.74800 49.11300 scale (grids/A): 2.174577 object centre (A): 41.24900 14.84000 45.67750 number of atom coordinates read : 2056 total number of charged atoms : 1921 net assigned charge : 5.931007 assigned positive charge : 312.1541 centred at (gu) : 90.13060 89.20281 87.73067 assigned negative charge : -306.2232 centred at (gu) : 90.62172 89.38322 87.78200 start vw surface at 0.1300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 78092 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16713 grid for indexing accessible points = 1.400000 m= 32158 mr = 56119 m= 6733 mr = 24938 m= 726 mr = 4621 m= 22 mr = 439 m= 0 mr = 4 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 31610 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 46 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 15284 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) : 0.7248590 object centre at (A) : 41.24900 14.84000 45.67750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4842622E-02 5.4948606E-02 midg,1,midg; midg,igrid,midg 3.4266669E-02 2.0408058E-03 1,midg,midg; igrid,midg,midg 4.7616798E-02 2.3206934E-02 gauss-seidel spectral radius is 0.9988745 estimated iterations to convergence 236 setup time was (sec) 0.8600000 now iterating at: 06:19:33 rms-change max change #iterations 4.790113 175.5779 at 10iterations 2.397171 83.09731 at 20iterations 1.215034 39.36626 at 30iterations 0.6109443 17.88074 at 40iterations 0.3071065 9.513124 at 50iterations 0.1554971 4.629393 at 60iterations 7.8026786E-02 2.213783 at 70iterations 3.9429855E-02 1.268390 at 80iterations 1.9888507E-02 0.5965109 at 90iterations 1.0089536E-02 0.2784557 at 100iterations 5.1330710E-03 0.1673145 at 110iterations 2.6371453E-03 7.7173233E-02 at 120iterations finished qdiffx linear iterations at : 06:19:40 total time elapsed so far: 7.260000 # loops : 120 mean,max change (kT/e) : 2.6371453E-03 7.7173233E-02 energy calculations done at 7.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.440000 DelPhi exited at 06:19:40 7.440u 0.207s 0:08.10 94.3% 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 06:19:40 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 = 2056 !!! WARNING: GLM 175 has a net charge of -0.0940 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 3.261866 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): 18.11300 64.38500 ymin,ymax (A): -3.534000 33.21400 zmin,zma (A): 21.12100 70.23400 x,y,z range (A): 46.27200 36.74800 49.11300 scale (grids/A): 3.261866 object centre (A): 41.24900 14.84000 45.67750 number of atom coordinates read : 2056 total number of charged atoms : 1921 net assigned charge : 5.931007 assigned positive charge : 312.1541 centred at (gu) : 90.19586 88.80433 86.59599 assigned negative charge : -306.2232 centred at (gu) : 90.93264 89.07486 86.67296 start vw surface at 0.1400000 fill in re-entrant regions at 0.8200000 boundary points on vw surface= 179558 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16713 grid for indexing accessible points = 1.400000 m= 99448 mr = 134630 m= 41981 mr = 83634 m= 12932 mr = 34990 m= 2842 mr = 10220 m= 386 mr = 2159 m= 9 mr = 280 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.830000 number of dielectric boundary points 71243 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.960000 number of grid points assigned charge 15368 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) : 2.174577 object centre at (A) : 41.24900 14.84000 45.67750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2068009 0.4691629 midg,1,midg; midg,igrid,midg 0.2699493 1.7852409E-02 1,midg,midg; igrid,midg,midg 0.3548441 0.3969623 gauss-seidel spectral radius is 0.9993039 estimated iterations to convergence 299 setup time was (sec) 2.130000 now iterating at: 06:19:43 rms-change max change #iterations 10.52760 405.4955 at 10iterations 6.240563 132.9808 at 20iterations 3.694138 69.27802 at 30iterations 2.190731 45.13648 at 40iterations 1.292533 21.89779 at 50iterations 0.7605416 13.49633 at 60iterations 0.4489614 8.557169 at 70iterations 0.2641918 4.813463 at 80iterations 0.1553624 2.561487 at 90iterations 9.1518901E-02 1.563559 at 100iterations 5.4065708E-02 0.9665375 at 110iterations 3.1902593E-02 0.5363731 at 120iterations 1.9092783E-02 0.3677387 at 130iterations 1.1544395E-02 0.2110462 at 140iterations 7.1829967E-03 0.1242714 at 150iterations 4.6599824E-03 8.9393616E-02 at 160iterations 3.1782659E-03 6.1977386E-02 at 170iterations 2.3018164E-03 4.5612335E-02 at 180iterations finished qdiffx linear iterations at : 06:19:53 total time elapsed so far: 12.44000 # loops : 180 mean,max change (kT/e) : 2.3018164E-03 4.5612335E-02 energy calculations done at 12.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.62000 DelPhi exited at 06:19:54 12.623u 0.220s 0:13.14 97.7% 0+0k 0+0io 0pf+0w