Sat Oct 8 18:29:58 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 18:29:58 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2425 !!! WARNING: HIR 64 has a net charge of 0.5140 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 421 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6631398 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): -32.00000 17.69500 ymin,ymax (A): -23.80600 23.36000 zmin,zma (A): -12.16900 41.51500 x,y,z range (A): 49.69500 47.16600 53.68401 scale (grids/A): 0.6631398 object centre (A): -7.152500 -0.2230005 14.67300 number of atom coordinates read : 2425 total number of charged atoms : 2304 net assigned charge : 2.420008 assigned positive charge : 368.9633 centred at (gu) : 88.75688 89.18980 89.89790 assigned negative charge : -366.5437 centred at (gu) : 88.63743 89.22289 89.81746 start vw surface at 0.1500000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7225 nv = 96 ne = 84 npr = 49931 no. pairs analyzed = 49931 no. exposed pairs = 2844 no. arc points = 20463 no. surface atoms = 953 nbur = 1472 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 421 mr = 4179 m= 3 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 252 time to turn everything in is 0.3800000 number of dielectric boundary points 3402 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1930 ## 176 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 8424 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.6015444E-09 2.2625608E-08 midg,1,midg; midg,igrid,midg 1.6149126E-08 3.0250216E-10 1,midg,midg; igrid,midg,midg -2.2862526E-08 2.3824906E-08 gauss-seidel spectral radius is 0.9881968 estimated iterations to convergence 75 setup time was (sec) 0.7100000 now iterating at: 18:29:59 rms-change max change #iterations 0.1632306 22.06511 at 10iterations 1.7827157E-02 2.520071 at 20iterations 1.9022909E-03 0.2779541 at 30iterations 2.0710360E-04 2.8499603E-02 at 40iterations 2.2436674E-05 3.1099319E-03 at 50iterations finished qdiffx linear iterations at : 18:30:02 total time elapsed so far: 4.210000 # loops : 50 mean,max change (kT/e) : 2.2436674E-05 3.1099319E-03 energy calculations done at 4.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.430000 DelPhi exited at 18:30:03 4.437u 0.433s 0:05.12 94.9% 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 18:30:03 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2425 !!! WARNING: HIR 64 has a net charge of 0.5140 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 421 has a net charge of 1.4000 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: 1.989419 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): -32.00000 17.69500 ymin,ymax (A): -23.80600 23.36000 zmin,zma (A): -12.16900 41.51500 x,y,z range (A): 49.69500 47.16600 53.68401 scale (grids/A): 1.989419 object centre (A): -7.152500 -0.2230005 14.67300 number of atom coordinates read : 2425 total number of charged atoms : 2304 net assigned charge : 2.420008 assigned positive charge : 368.9633 centred at (gu) : 86.27009 87.56932 89.69348 assigned negative charge : -366.5437 centred at (gu) : 85.91202 87.66853 89.45212 start vw surface at 0.1400000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 77502 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20463 grid for indexing accessible points = 1.400000 m= 29891 mr = 54795 m= 5136 mr = 22938 m= 339 mr = 3467 m= 9 mr = 153 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 7173 time to turn everything in is 0.7800000 number of dielectric boundary points 31524 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 104 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 18220 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) : 0.6631398 object centre at (A) : -7.152500 -0.2230005 14.67300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2849852E-02 1.4326736E-02 midg,1,midg; midg,igrid,midg 1.9236021E-02 2.6924312E-03 1,midg,midg; igrid,midg,midg -4.7829836E-03 4.9836852E-02 gauss-seidel spectral radius is 0.9987281 estimated iterations to convergence 222 setup time was (sec) 1.100000 now iterating at: 18:30:05 rms-change max change #iterations 4.466889 204.4516 at 10iterations 2.150612 68.67831 at 20iterations 1.031373 36.53155 at 30iterations 0.4967943 14.45229 at 40iterations 0.2396832 9.122929 at 50iterations 0.1150284 3.536053 at 60iterations 5.5517133E-02 1.619427 at 70iterations 2.6656508E-02 0.7872620 at 80iterations 1.2796602E-02 0.3852386 at 90iterations 6.1682072E-03 0.2111664 at 100iterations 2.9664256E-03 9.7385406E-02 at 110iterations 1.4266189E-03 4.5616150E-02 at 120iterations finished qdiffx linear iterations at : 18:30:14 total time elapsed so far: 10.05000 # loops : 120 mean,max change (kT/e) : 1.4266189E-03 4.5616150E-02 energy calculations done at 10.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.26000 DelPhi exited at 18:30:14 10.264u 0.496s 0:11.06 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 18:30:14 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2425 !!! WARNING: HIR 64 has a net charge of 0.5140 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 421 has a net charge of 1.4000 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: 2.984129 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): -32.00000 17.69500 ymin,ymax (A): -23.80600 23.36000 zmin,zma (A): -12.16900 41.51500 x,y,z range (A): 49.69500 47.16600 53.68401 scale (grids/A): 2.984129 object centre (A): -7.152500 -0.2230005 14.67300 number of atom coordinates read : 2425 total number of charged atoms : 2304 net assigned charge : 2.420008 assigned positive charge : 368.9633 centred at (gu) : 84.40517 86.35386 89.53992 assigned negative charge : -366.5437 centred at (gu) : 83.86798 86.50267 89.17806 start vw surface at 0.1500000 fill in re-entrant regions at 0.6800000 boundary points on vw surface= 178741 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20463 grid for indexing accessible points = 1.400000 m= 94988 mr = 131864 m= 36651 mr = 79695 m= 9356 mr = 30313 m= 1483 mr = 7405 m= 118 mr = 1075 m= 1 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 1.260000 no. cavity mid-points inaccessible to solvent = 23012 time to turn everything in is 2.080000 number of dielectric boundary points 70925 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.230000 number of grid points assigned charge 18432 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) : 1.989419 object centre at (A) : -7.152500 -0.2230005 14.67300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1356726 0.1837015 midg,1,midg; midg,igrid,midg 0.2225565 -8.5196933E-03 1,midg,midg; igrid,midg,midg 6.2487051E-02 0.5762606 gauss-seidel spectral radius is 0.9992755 estimated iterations to convergence 293 setup time was (sec) 2.440000 now iterating at: 18:30:17 rms-change max change #iterations 10.19083 491.2379 at 10iterations 5.891639 120.5642 at 20iterations 3.420558 66.87988 at 30iterations 1.982162 35.30023 at 40iterations 1.145027 20.65306 at 50iterations 0.6618401 11.28192 at 60iterations 0.3833278 6.665855 at 70iterations 0.2221166 4.242975 at 80iterations 0.1281489 2.235683 at 90iterations 7.4181892E-02 1.376275 at 100iterations 4.2784359E-02 0.7165222 at 110iterations 2.4727108E-02 0.4354286 at 120iterations 1.4287690E-02 0.2497330 at 130iterations 8.2596252E-03 0.1423159 at 140iterations 4.7851559E-03 8.4476471E-02 at 150iterations 2.7652076E-03 5.0253868E-02 at 160iterations 1.6006019E-03 2.9212952E-02 at 170iterations 9.2978787E-04 1.6008794E-02 at 180iterations finished qdiffx linear iterations at : 18:30:32 total time elapsed so far: 17.52000 # loops : 180 mean,max change (kT/e) : 9.2978787E-04 1.6008794E-02 energy calculations done at 17.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.73000 DelPhi exited at 18:30:33 17.730u 0.491s 0:18.51 98.4% 0+0k 0+0io 0pf+0w