Wed Dec 28 11:03:26 PST 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 Wed Dec 28 2011 at 11:03:27 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1944 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: GLN 7 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: GLY 67 has a net charge of 0.2480 !!! WARNING: ASN 82 has a net charge of -0.6880 !!! WARNING: ARG 86 has a net charge of -0.4460 !!! WARNING: ASN 87 has a net charge of -0.6880 !!! WARNING: GLN 91 has a net charge of -0.6880 !!! WARNING: ASN 97 has a net charge of -0.6880 !!! WARNING: GLN 100 has a net charge of -0.6880 !!! WARNING: GLN 105 has a net charge of -0.6880 !!! WARNING: ARG 106 has a net charge of -0.4460 !!! WARNING: GLN 116 has a net charge of -0.6880 !!! WARNING: ARG 139 has a net charge of -0.4460 !!! WARNING: ARG 155 has a net charge of -0.4460 !!! WARNING: GLN 156 has a net charge of -0.6880 !!! WARNING: GLN 159 has a net charge of -0.6880 !!! WARNING: GLY 165 has a net charge of 0.2480 !!! WARNING: ASN 180 has a net charge of -0.6880 !!! WARNING: ARG 184 has a net charge of -0.4460 !!! WARNING: ASN 185 has a net charge of -0.6880 !!! WARNING: GLN 189 has a net charge of -0.6880 !!! WARNING: ASN 195 has a net charge of -0.6880 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: 0.6234567 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): -35.14900 10.12600 ymin,ymax (A): 1.130000 41.35300 zmin,zma (A): -0.6190000 56.48200 x,y,z range (A): 45.27500 40.22300 57.10100 scale (grids/A): 0.6234567 object centre (A): -12.51150 21.24150 27.93150 number of atom coordinates read : 1944 total number of charged atoms : 1744 net assigned charge : -21.45602 assigned positive charge : 261.7885 centred at (gu) : 90.38614 89.55595 89.95641 assigned negative charge : -283.2443 centred at (gu) : 90.29057 89.71436 89.99477 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5198 nv = 96 ne = 84 npr = 39548 no. pairs analyzed = 39548 no. exposed pairs = 2500 no. arc points = 17559 no. surface atoms = 853 nbur = 1091 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 295 mr = 2779 m= 0 mr = 41 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 2673 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1725 ## 147 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 6010 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7353683E-08 -2.1113451E-08 midg,1,midg; midg,igrid,midg -1.1926171E-08 -2.5353941E-08 1,midg,midg; igrid,midg,midg -2.2489717E-08 -1.5357767E-08 gauss-seidel spectral radius is 0.9866214 estimated iterations to convergence 71 setup time was (sec) 0.4800000 now iterating at: 11:03:28 rms-change max change #iterations 0.1168273 20.12052 at 10iterations 1.0910147E-02 1.825930 at 20iterations 1.0067112E-03 0.1702957 at 30iterations 9.3217699E-05 1.6006470E-02 at 40iterations 8.7737744E-06 1.4572144E-03 at 50iterations finished qdiffx linear iterations at : 11:03:30 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 8.7737744E-06 1.4572144E-03 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.700000 DelPhi exited at 11:03:34 3.699u 0.567s 0:07.01 60.6% 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 Wed Dec 28 2011 at 11:03:34 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1944 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: GLN 7 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: GLY 67 has a net charge of 0.2480 !!! WARNING: ASN 82 has a net charge of -0.6880 !!! WARNING: ARG 86 has a net charge of -0.4460 !!! WARNING: ASN 87 has a net charge of -0.6880 !!! WARNING: GLN 91 has a net charge of -0.6880 !!! WARNING: ASN 97 has a net charge of -0.6880 !!! WARNING: GLN 100 has a net charge of -0.6880 !!! WARNING: GLN 105 has a net charge of -0.6880 !!! WARNING: ARG 106 has a net charge of -0.4460 !!! WARNING: GLN 116 has a net charge of -0.6880 !!! WARNING: ARG 139 has a net charge of -0.4460 !!! WARNING: ARG 155 has a net charge of -0.4460 !!! WARNING: GLN 156 has a net charge of -0.6880 !!! WARNING: GLN 159 has a net charge of -0.6880 !!! WARNING: GLY 165 has a net charge of 0.2480 !!! WARNING: ASN 180 has a net charge of -0.6880 !!! WARNING: ARG 184 has a net charge of -0.4460 !!! WARNING: ASN 185 has a net charge of -0.6880 !!! WARNING: GLN 189 has a net charge of -0.6880 !!! WARNING: ASN 195 has a net charge of -0.6880 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.870370 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): -35.14900 10.12600 ymin,ymax (A): 1.130000 41.35300 zmin,zma (A): -0.6190000 56.48200 x,y,z range (A): 45.27500 40.22300 57.10100 scale (grids/A): 1.870370 object centre (A): -12.51150 21.24150 27.93150 number of atom coordinates read : 1944 total number of charged atoms : 1744 net assigned charge : -21.45602 assigned positive charge : 261.7885 centred at (gu) : 91.15891 88.66810 89.86932 assigned negative charge : -283.2443 centred at (gu) : 90.87193 89.14323 89.98457 start vw surface at 0.1200000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 55983 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17559 grid for indexing accessible points = 1.400000 m= 20677 mr = 38182 m= 3232 mr = 15291 m= 221 mr = 2049 m= 2 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 330 time to turn everything in is 0.4000000 number of dielectric boundary points 24520 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 116 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 13715 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) : 0.6234567 object centre at (A) : -12.51150 21.24150 27.93150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.0528415E-02 -6.3190103E-02 midg,1,midg; midg,igrid,midg -2.1021247E-02 -3.8054932E-02 1,midg,midg; igrid,midg,midg -2.4610467E-02 -3.3074506E-02 gauss-seidel spectral radius is 0.9985120 estimated iterations to convergence 206 setup time was (sec) 0.6700000 now iterating at: 11:03:35 rms-change max change #iterations 3.413409 143.0990 at 10iterations 1.554700 65.18008 at 20iterations 0.6996741 26.72434 at 30iterations 0.3167441 11.57859 at 40iterations 0.1433445 5.211651 at 50iterations 6.4853773E-02 2.331882 at 60iterations 2.9309127E-02 1.098457 at 70iterations 1.3314500E-02 0.4677868 at 80iterations 6.0326639E-03 0.2333298 at 90iterations 2.7173571E-03 0.1030025 at 100iterations 1.2284848E-03 4.4718742E-02 at 110iterations 5.5884977E-04 2.0515442E-02 at 120iterations finished qdiffx linear iterations at : 11:03:42 total time elapsed so far: 7.270000 # loops : 120 mean,max change (kT/e) : 5.5884977E-04 2.0515442E-02 energy calculations done at 7.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.690000 DelPhi exited at 11:03:45 7.696u 0.575s 0:10.47 78.8% 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 Wed Dec 28 2011 at 11:03:45 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1944 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: GLN 7 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: GLY 67 has a net charge of 0.2480 !!! WARNING: ASN 82 has a net charge of -0.6880 !!! WARNING: ARG 86 has a net charge of -0.4460 !!! WARNING: ASN 87 has a net charge of -0.6880 !!! WARNING: GLN 91 has a net charge of -0.6880 !!! WARNING: ASN 97 has a net charge of -0.6880 !!! WARNING: GLN 100 has a net charge of -0.6880 !!! WARNING: GLN 105 has a net charge of -0.6880 !!! WARNING: ARG 106 has a net charge of -0.4460 !!! WARNING: GLN 116 has a net charge of -0.6880 !!! WARNING: ARG 139 has a net charge of -0.4460 !!! WARNING: ARG 155 has a net charge of -0.4460 !!! WARNING: GLN 156 has a net charge of -0.6880 !!! WARNING: GLN 159 has a net charge of -0.6880 !!! WARNING: GLY 165 has a net charge of 0.2480 !!! WARNING: ASN 180 has a net charge of -0.6880 !!! WARNING: ARG 184 has a net charge of -0.4460 !!! WARNING: ASN 185 has a net charge of -0.6880 !!! WARNING: GLN 189 has a net charge of -0.6880 !!! WARNING: ASN 195 has a net charge of -0.6880 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: 2.805555 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): -35.14900 10.12600 ymin,ymax (A): 1.130000 41.35300 zmin,zma (A): -0.6190000 56.48200 x,y,z range (A): 45.27500 40.22300 57.10100 scale (grids/A): 2.805555 object centre (A): -12.51150 21.24150 27.93150 number of atom coordinates read : 1944 total number of charged atoms : 1744 net assigned charge : -21.45602 assigned positive charge : 261.7885 centred at (gu) : 91.73840 88.00222 89.80411 assigned negative charge : -283.2443 centred at (gu) : 91.30795 88.71494 89.97684 start vw surface at 0.1400000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 129257 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17559 grid for indexing accessible points = 1.400000 m= 66495 mr = 92438 m= 24340 mr = 54425 m= 5621 mr = 19692 m= 791 mr = 4220 m= 46 mr = 499 m= 0 mr = 11 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 1133 time to turn everything in is 1.090000 number of dielectric boundary points 55265 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.220000 number of grid points assigned charge 13951 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) : 1.870370 object centre at (A) : -12.51150 21.24150 27.93150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7453060 -0.9399121 midg,1,midg; midg,igrid,midg -0.2326960 -0.4267386 1,midg,midg; igrid,midg,midg -0.2541905 -0.3504815 gauss-seidel spectral radius is 0.9992093 estimated iterations to convergence 281 setup time was (sec) 1.370000 now iterating at: 11:03:46 rms-change max change #iterations 8.089828 299.6792 at 10iterations 4.629131 114.9373 at 20iterations 2.620086 60.38985 at 30iterations 1.484940 33.16002 at 40iterations 0.8391038 19.42534 at 50iterations 0.4733827 9.864773 at 60iterations 0.2661452 5.731248 at 70iterations 0.1507828 3.121220 at 80iterations 8.4766783E-02 1.970713 at 90iterations 4.7838546E-02 1.038927 at 100iterations 2.6967604E-02 0.5421562 at 110iterations 1.5144909E-02 0.3136539 at 120iterations 8.5330531E-03 0.1895180 at 130iterations 4.8056184E-03 0.1061325 at 140iterations 2.7078530E-03 5.7952881E-02 at 150iterations 1.5251805E-03 3.4446716E-02 at 160iterations 8.5913145E-04 1.7865181E-02 at 170iterations 4.8373654E-04 9.8037720E-03 at 180iterations finished qdiffx linear iterations at : 11:03:57 total time elapsed so far: 12.02000 # loops : 180 mean,max change (kT/e) : 4.8373654E-04 9.8037720E-03 energy calculations done at 12.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.19000 DelPhi exited at 11:03:57 12.192u 0.199s 0:12.73 97.2% 0+0k 0+0io 0pf+0w