Sun Oct 9 19:49:01 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 Sun Oct 9 2011 at 19:49:01 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3511 !!! WARNING: LLP 1 has a net charge of 1.3200 !!! WARNING: LLP 2 has a net charge of 0.2100 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5646044 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): 6.403000 66.66400 ymin,ymax (A): 1.790000 62.07600 zmin,zma (A): -0.8820000 62.17100 x,y,z range (A): 60.26100 60.28600 63.05300 scale (grids/A): 0.5646044 object centre (A): 36.53350 31.93300 30.64450 number of atom coordinates read : 3511 total number of charged atoms : 3354 net assigned charge : -0.4699764 assigned positive charge : 529.6758 centred at (gu) : 88.64036 88.35093 88.65913 assigned negative charge : -530.1475 centred at (gu) : 88.58163 88.40464 88.64924 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7652 nv = 96 ne = 84 npr = 67625 no. pairs analyzed = 67625 no. exposed pairs = 4717 no. arc points = 32825 no. surface atoms = 1584 nbur = 1927 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 = 1.540000 m= 382 mr = 3962 m= 0 mr = 18 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 4054 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3252 ## 354 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9638 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.9152589E-10 6.7805983E-11 midg,1,midg; midg,igrid,midg 1.1512494E-09 -5.9903155E-10 1,midg,midg; igrid,midg,midg -1.3546954E-09 6.0481675E-10 gauss-seidel spectral radius is 0.9838676 estimated iterations to convergence 65 setup time was (sec) 0.5600000 now iterating at: 19:49:01 rms-change max change #iterations 9.5306046E-02 13.63284 at 10iterations 8.4866565E-03 1.306557 at 20iterations 2.9881254E-03 0.3517303 at 30iterations 1.8634296E-03 0.2208805 at 40iterations 1.1895546E-03 0.1436920 at 50iterations finished qdiffx linear iterations at : 19:49:04 total time elapsed so far: 2.990000 # loops : 50 mean,max change (kT/e) : 1.1895546E-03 0.1436920 energy calculations done at 2.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.160000 DelPhi exited at 19:49:04 3.165u 0.137s 0:03.58 91.8% 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 Sun Oct 9 2011 at 19:49:04 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3511 !!! WARNING: LLP 1 has a net charge of 1.3200 !!! WARNING: LLP 2 has a net charge of 0.2100 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.693813 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): 6.403000 66.66400 ymin,ymax (A): 1.790000 62.07600 zmin,zma (A): -0.8820000 62.17100 x,y,z range (A): 60.26100 60.28600 63.05300 scale (grids/A): 1.693813 object centre (A): 36.53350 31.93300 30.64450 number of atom coordinates read : 3511 total number of charged atoms : 3354 net assigned charge : -0.4699764 assigned positive charge : 529.6758 centred at (gu) : 85.91994 85.05176 85.97639 assigned negative charge : -530.1475 centred at (gu) : 85.74412 85.21332 85.94702 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 84395 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32825 grid for indexing accessible points = 1.400000 m= 29042 mr = 57810 m= 3867 mr = 19928 m= 130 mr = 1908 m= 2 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 37766 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 302 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 25901 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) : 0.5646044 object centre at (A) : 36.53350 31.93300 30.64450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6796855E-02 -8.1610708E-03 midg,1,midg; midg,igrid,midg 1.0948185E-02 -5.3740479E-03 1,midg,midg; igrid,midg,midg -6.9377362E-03 -1.9105264E-03 gauss-seidel spectral radius is 0.9983836 estimated iterations to convergence 197 setup time was (sec) 0.8400000 now iterating at: 19:49:05 rms-change max change #iterations 4.016031 157.2434 at 10iterations 1.762648 62.30372 at 20iterations 0.7719982 27.17834 at 30iterations 0.3378486 10.64653 at 40iterations 0.1489503 4.948184 at 50iterations 6.6017717E-02 2.244037 at 60iterations 2.9479442E-02 1.085191 at 70iterations 1.3843376E-02 0.4096699 at 80iterations 7.2502908E-03 0.2350674 at 90iterations 4.6721683E-03 0.1400928 at 100iterations 3.5637058E-03 9.4955444E-02 at 110iterations 2.9348545E-03 7.4249268E-02 at 120iterations finished qdiffx linear iterations at : 19:49:12 total time elapsed so far: 8.050000 # loops : 120 mean,max change (kT/e) : 2.9348545E-03 7.4249268E-02 energy calculations done at 8.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.250000 DelPhi exited at 19:49:13 8.248u 0.166s 0:08.69 96.6% 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 Sun Oct 9 2011 at 19:49:13 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3511 !!! WARNING: LLP 1 has a net charge of 1.3200 !!! WARNING: LLP 2 has a net charge of 0.2100 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: 2.540720 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): 6.403000 66.66400 ymin,ymax (A): 1.790000 62.07600 zmin,zma (A): -0.8820000 62.17100 x,y,z range (A): 60.26100 60.28600 63.05300 scale (grids/A): 2.540720 object centre (A): 36.53350 31.93300 30.64450 number of atom coordinates read : 3511 total number of charged atoms : 3354 net assigned charge : -0.4699764 assigned positive charge : 529.6758 centred at (gu) : 83.87949 82.57721 83.96444 assigned negative charge : -530.1475 centred at (gu) : 83.61620 82.81993 83.92041 start vw surface at 0.1600000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 195409 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32825 grid for indexing accessible points = 1.400000 m= 96625 mr = 141107 m= 31692 mr = 76409 m= 6413 mr = 23647 m= 577 mr = 4169 m= 12 mr = 232 m= 0 mr = 0 time to grow re-entrant surface = 0.8799999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.460000 number of dielectric boundary points 85164 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.590000 number of grid points assigned charge 26806 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) : 1.693813 object centre at (A) : 36.53350 31.93300 30.64450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2146518 -6.8649061E-02 midg,1,midg; midg,igrid,midg 0.1408077 -7.8457341E-02 1,midg,midg; igrid,midg,midg -7.9295225E-03 -7.0491955E-02 gauss-seidel spectral radius is 0.9992213 estimated iterations to convergence 283 setup time was (sec) 1.740000 now iterating at: 19:49:15 rms-change max change #iterations 10.46364 318.5303 at 10iterations 6.206515 171.9865 at 20iterations 3.638884 86.48981 at 30iterations 2.119466 49.21624 at 40iterations 1.228772 27.52279 at 50iterations 0.7070684 17.93893 at 60iterations 0.4069449 8.890270 at 70iterations 0.2332994 4.735264 at 80iterations 0.1336568 2.597655 at 90iterations 7.6567754E-02 1.439945 at 100iterations 4.3895114E-02 0.7977371 at 110iterations 2.5229217E-02 0.5468330 at 120iterations 1.4578808E-02 0.2982650 at 130iterations 8.5815946E-03 0.1805649 at 140iterations 5.2734381E-03 0.1143112 at 150iterations 3.4580515E-03 8.2752228E-02 at 160iterations 2.4896904E-03 4.7473907E-02 at 170iterations 1.9724406E-03 3.4269333E-02 at 180iterations finished qdiffx linear iterations at : 19:49:24 total time elapsed so far: 11.26000 # loops : 180 mean,max change (kT/e) : 1.9724406E-03 3.4269333E-02 energy calculations done at 11.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.44000 DelPhi exited at 19:49:25 11.442u 0.189s 0:11.89 97.7% 0+0k 0+0io 0pf+0w