Sat Oct 8 16:30:25 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 16:30:25 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2457 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: ASP 931 has a net charge of -2.0000 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: 0.6546164 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): -2.834000 45.22400 ymin,ymax (A): -15.96800 28.94000 zmin,zma (A): -17.73600 36.64700 x,y,z range (A): 48.05800 44.90800 54.38300 scale (grids/A): 0.6546164 object centre (A): 21.19500 6.486001 9.455500 number of atom coordinates read : 2457 total number of charged atoms : 2360 net assigned charge : 1.900001 assigned positive charge : 365.7758 centred at (gu) : 90.91030 89.09532 90.57832 assigned negative charge : -363.8767 centred at (gu) : 91.00465 89.30883 90.65829 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7042 nv = 96 ne = 84 npr = 50077 no. pairs analyzed = 50077 no. exposed pairs = 2995 no. arc points = 20961 no. surface atoms = 1016 nbur = 1441 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 426 mr = 3964 m= 2 mr = 78 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.3200000 number of dielectric boundary points 3428 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2086 ## 198 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8491 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4952423E-08 -1.0102857E-08 midg,1,midg; midg,igrid,midg 4.5790287E-08 -2.5613021E-08 1,midg,midg; igrid,midg,midg 1.5824657E-08 -1.3747987E-08 gauss-seidel spectral radius is 0.9878938 estimated iterations to convergence 74 setup time was (sec) 0.6000000 now iterating at: 16:30:26 rms-change max change #iterations 0.1552238 23.42033 at 10iterations 1.6005041E-02 2.354214 at 20iterations 1.6896995E-03 0.2599182 at 30iterations 1.8714488E-04 2.6315689E-02 at 40iterations 2.3456827E-05 3.2253265E-03 at 50iterations finished qdiffx linear iterations at : 16:30:29 total time elapsed so far: 3.940000 # loops : 50 mean,max change (kT/e) : 2.3456827E-05 3.2253265E-03 energy calculations done at 3.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.130000 DelPhi exited at 16:30:30 4.130u 0.284s 0:04.72 93.4% 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 16:30:30 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2457 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: ASP 931 has a net charge of -2.0000 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: 1.963849 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): -2.834000 45.22400 ymin,ymax (A): -15.96800 28.94000 zmin,zma (A): -17.73600 36.64700 x,y,z range (A): 48.05800 44.90800 54.38300 scale (grids/A): 1.963849 object centre (A): 21.19500 6.486001 9.455500 number of atom coordinates read : 2457 total number of charged atoms : 2360 net assigned charge : 1.900001 assigned positive charge : 365.7758 centred at (gu) : 92.73030 87.28544 91.73441 assigned negative charge : -363.8767 centred at (gu) : 93.01407 87.92633 91.97471 start vw surface at 0.1600000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 75959 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20961 grid for indexing accessible points = 1.400000 m= 28235 mr = 53286 m= 5223 mr = 21203 m= 369 mr = 3654 m= 7 mr = 172 m= 0 mr = 1 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 1215 time to turn everything in is 0.6900000 number of dielectric boundary points 31477 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 153 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 18649 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) : 0.6546164 object centre at (A) : 21.19500 6.486001 9.455500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2813544E-02 -1.4592082E-02 midg,1,midg; midg,igrid,midg 3.0341428E-02 -1.5806079E-02 1,midg,midg; igrid,midg,midg 6.7390278E-03 -5.5683389E-02 gauss-seidel spectral radius is 0.9986969 estimated iterations to convergence 219 setup time was (sec) 0.9900000 now iterating at: 16:30:31 rms-change max change #iterations 4.394308 199.2474 at 10iterations 2.085777 75.98085 at 20iterations 0.9939471 41.27993 at 30iterations 0.4742055 15.84118 at 40iterations 0.2258462 7.725754 at 50iterations 0.1078045 3.241317 at 60iterations 5.1291615E-02 1.745857 at 70iterations 2.4437899E-02 0.8304634 at 80iterations 1.1678133E-02 0.3666821 at 90iterations 5.5563645E-03 0.1818295 at 100iterations 2.6590982E-03 9.3583107E-02 at 110iterations 1.2727225E-03 4.4506073E-02 at 120iterations finished qdiffx linear iterations at : 16:30:40 total time elapsed so far: 9.440000 # loops : 120 mean,max change (kT/e) : 1.2727225E-03 4.4506073E-02 energy calculations done at 9.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.620000 DelPhi exited at 16:30:40 9.622u 0.325s 0:10.30 96.5% 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 Sat Oct 8 2011 at 16:30:40 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2457 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: ASP 931 has a net charge of -2.0000 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: 2.945774 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): -2.834000 45.22400 ymin,ymax (A): -15.96800 28.94000 zmin,zma (A): -17.73600 36.64700 x,y,z range (A): 48.05800 44.90800 54.38300 scale (grids/A): 2.945774 object centre (A): 21.19500 6.486001 9.455500 number of atom coordinates read : 2457 total number of charged atoms : 2360 net assigned charge : 1.900001 assigned positive charge : 365.7758 centred at (gu) : 94.09524 85.92796 92.60149 assigned negative charge : -363.8767 centred at (gu) : 94.52104 86.88950 92.96204 start vw surface at 0.1600000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 175868 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20961 grid for indexing accessible points = 1.400000 m= 89711 mr = 129028 m= 34833 mr = 74012 m= 9760 mr = 28857 m= 1575 mr = 7879 m= 138 mr = 1132 m= 3 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 4161 time to turn everything in is 1.770000 number of dielectric boundary points 70910 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.920000 number of grid points assigned charge 18875 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) : 1.963849 object centre at (A) : 21.19500 6.486001 9.455500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2117183 -0.2517427 midg,1,midg; midg,igrid,midg 0.2349686 -0.1497453 1,midg,midg; igrid,midg,midg 7.5674832E-02 -0.7402925 gauss-seidel spectral radius is 0.9992709 estimated iterations to convergence 292 setup time was (sec) 2.090000 now iterating at: 16:30:43 rms-change max change #iterations 10.09450 466.7032 at 10iterations 5.888793 124.2548 at 20iterations 3.422693 66.89053 at 30iterations 1.987180 38.71880 at 40iterations 1.151614 20.43575 at 50iterations 0.6685384 12.20643 at 60iterations 0.3863925 7.302803 at 70iterations 0.2232823 4.275926 at 80iterations 0.1288957 2.373970 at 90iterations 7.4569777E-02 1.287781 at 100iterations 4.3118283E-02 0.7570610 at 110iterations 2.4856053E-02 0.4786873 at 120iterations 1.4351371E-02 0.2564888 at 130iterations 8.2906559E-03 0.1511574 at 140iterations 4.7784904E-03 8.8473082E-02 at 150iterations 2.7681726E-03 4.5909882E-02 at 160iterations 1.6002741E-03 3.0155182E-02 at 170iterations 9.2841138E-04 1.6563416E-02 at 180iterations finished qdiffx linear iterations at : 16:30:57 total time elapsed so far: 16.12000 # loops : 180 mean,max change (kT/e) : 9.2841138E-04 1.6563416E-02 energy calculations done at 16.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.31000 DelPhi exited at 16:30:57 16.310u 0.323s 0:16.92 98.2% 0+0k 0+0io 0pf+0w