Sun Oct 9 17:08:54 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 Sun Oct 9 2011 at 17:08:54 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5276 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.5461882 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): 3.273000 67.73300 ymin,ymax (A): -8.563000 54.56800 zmin,zma (A): -2.179000 63.00000 x,y,z range (A): 64.46000 63.13100 65.17900 scale (grids/A): 0.5461882 object centre (A): 35.50300 23.00250 30.41050 number of atom coordinates read : 5276 total number of charged atoms : 5141 net assigned charge : 0.6350498 assigned positive charge : 815.7881 centred at (gu) : 88.17896 88.83354 89.35580 assigned negative charge : -815.1595 centred at (gu) : 88.06051 88.88922 89.30001 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 10069 nv = 96 ne = 84 npr = 107852 no. pairs analyzed = 107852 no. exposed pairs = 6083 no. arc points = 41554 no. surface atoms = 2073 nbur = 3203 mkacc time = 0.2500000 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 = 1.568000 m= 390 mr = 5669 m= 2 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 4778 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4186 ## 483 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 13356 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.2896272E-10 6.3159189E-10 midg,1,midg; midg,igrid,midg 9.9476127E-10 -4.6110163E-10 1,midg,midg; igrid,midg,midg -2.2287128E-09 9.4761976E-10 gauss-seidel spectral radius is 0.9828800 estimated iterations to convergence 63 setup time was (sec) 0.7400000 now iterating at: 17:08:55 rms-change max change #iterations 0.1056780 14.05632 at 10iterations 9.0095038E-03 1.443012 at 20iterations 2.3756507E-03 0.2739563 at 30iterations 1.0348773E-03 0.1080017 at 40iterations 4.7051269E-04 4.8278809E-02 at 50iterations finished qdiffx linear iterations at : 17:08:58 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 4.7051269E-04 4.8278809E-02 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 17:08:58 3.546u 0.167s 0:04.00 92.5% 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 Sun Oct 9 2011 at 17:08:58 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5276 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.638565 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): 3.273000 67.73300 ymin,ymax (A): -8.563000 54.56800 zmin,zma (A): -2.179000 63.00000 x,y,z range (A): 64.46000 63.13100 65.17900 scale (grids/A): 1.638565 object centre (A): 35.50300 23.00250 30.41050 number of atom coordinates read : 5276 total number of charged atoms : 5141 net assigned charge : 0.6350498 assigned positive charge : 815.7881 centred at (gu) : 84.53512 86.49908 88.06613 assigned negative charge : -815.1595 centred at (gu) : 84.18163 86.66752 87.89977 start vw surface at 0.2100000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 113698 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41554 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 37110 mr = 82434 m= 4033 mr = 26361 m= 117 mr = 1926 m= 0 mr = 10 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 221 time to turn everything in is 0.7900000 number of dielectric boundary points 44227 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 412 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 39408 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) : 0.5461882 object centre at (A) : 35.50300 23.00250 30.41050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.7445680E-02 -7.9973238E-03 midg,1,midg; midg,igrid,midg 2.6603252E-02 5.8352207E-03 1,midg,midg; igrid,midg,midg -1.8255249E-02 3.3085197E-03 gauss-seidel spectral radius is 0.9984002 estimated iterations to convergence 198 setup time was (sec) 1.080000 now iterating at: 17:08:59 rms-change max change #iterations 4.819445 158.5972 at 10iterations 2.118797 61.93318 at 20iterations 0.9308822 26.72319 at 30iterations 0.4118276 11.63801 at 40iterations 0.1819094 5.376967 at 50iterations 8.0616005E-02 2.268962 at 60iterations 3.5829443E-02 1.054756 at 70iterations 1.6358754E-02 0.4321556 at 80iterations 7.7683884E-03 0.2361832 at 90iterations 4.0311571E-03 0.1082592 at 100iterations 2.3857781E-03 6.5347672E-02 at 110iterations 1.5964867E-03 3.8757324E-02 at 120iterations finished qdiffx linear iterations at : 17:09:06 total time elapsed so far: 7.640000 # loops : 120 mean,max change (kT/e) : 1.5964867E-03 3.8757324E-02 energy calculations done at 7.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.820000 DelPhi exited at 17:09:07 7.827u 0.179s 0:08.28 96.4% 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 Sun Oct 9 2011 at 17:09:07 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5276 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.457847 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): 3.273000 67.73300 ymin,ymax (A): -8.563000 54.56800 zmin,zma (A): -2.179000 63.00000 x,y,z range (A): 64.46000 63.13100 65.17900 scale (grids/A): 2.457847 object centre (A): 35.50300 23.00250 30.41050 number of atom coordinates read : 5276 total number of charged atoms : 5141 net assigned charge : 0.6350498 assigned positive charge : 815.7881 centred at (gu) : 81.80236 84.74797 87.09863 assigned negative charge : -815.1595 centred at (gu) : 81.27213 85.00135 86.84981 start vw surface at 0.2300000 fill in re-entrant regions at 0.6600000 boundary points on vw surface= 264418 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41554 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 128112 mr = 200380 m= 37840 mr = 104016 m= 6478 mr = 28699 m= 497 mr = 4126 m= 12 mr = 217 m= 0 mr = 0 time to grow re-entrant surface = 1.190000 no. cavity mid-points inaccessible to solvent = 719 time to turn everything in is 1.990000 number of dielectric boundary points 99919 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 29 iepsmp to db, and charging done at 2.130000 number of grid points assigned charge 41067 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) : 1.638565 object centre at (A) : 35.50300 23.00250 30.41050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4112494 -0.2304818 midg,1,midg; midg,igrid,midg 0.2992201 2.5472937E-02 1,midg,midg; igrid,midg,midg -0.4122567 2.9346291E-02 gauss-seidel spectral radius is 0.9992442 estimated iterations to convergence 287 setup time was (sec) 2.300000 now iterating at: 17:09:09 rms-change max change #iterations 12.26827 308.8684 at 10iterations 7.203329 193.4611 at 20iterations 4.201410 88.38136 at 30iterations 2.442214 44.90557 at 40iterations 1.412282 26.96935 at 50iterations 0.8157295 13.90857 at 60iterations 0.4693254 9.503531 at 70iterations 0.2700193 4.463105 at 80iterations 0.1553180 2.665466 at 90iterations 8.9301832E-02 1.512209 at 100iterations 5.1289953E-02 0.8318481 at 110iterations 2.9652832E-02 0.4915161 at 120iterations 1.7234325E-02 0.2917633 at 130iterations 1.0181444E-02 0.1580744 at 140iterations 6.1685224E-03 0.1052666 at 150iterations 3.9121979E-03 6.5673828E-02 at 160iterations 2.6470255E-03 4.3472290E-02 at 170iterations 1.9220886E-03 2.9907227E-02 at 180iterations finished qdiffx linear iterations at : 17:09:20 total time elapsed so far: 12.81000 # loops : 180 mean,max change (kT/e) : 1.9220886E-03 2.9907227E-02 energy calculations done at 12.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.00000 DelPhi exited at 17:09:20 13.002u 0.176s 0:13.45 97.9% 0+0k 0+0io 0pf+0w