1
                 Chemistry at HARvard Macromolecular Mechanics
                   (CHARMM) - Developmental Version 35b2   February 15, 2008   
       Copyright(c) 1984-2001  President and Fellows of Harvard College
                              All Rights Reserved
      Current operating system: Linux-2.6.28-17-generic(x86_64)@morgan.ucsd.
                 Created on  3/15/10 at  9:38:41 by user: rok         

            Maximum number of ATOMS:     25140, and RESidues:       14000
            Current HEAP size:         2048000, and STACK size:    500000

 RDTITL> * APBS_VIS.INP
 RDTITL> * EXTERNAL FILES: TOP_ALL22_PROT.INP, PAR_ALL22_PROT.INP AND RADIUS.STR
 RDTITL> * $ID: APBS_VIS.INP,V 1.2 2005/06/20 21:40:02 ROK EXP $
 RDTITL>  
  
 CHARMM>     
  
 CHARMM>    !if ?apbs .ne. 1 then stop
 CHARMM>     
  
 CHARMM>    stream datadir.def
 VOPEN> Attempting to open::datadir.def::
 OPNLGU> Unit 99 opened for READONLY access to /home/rok/Sandbox-100309/iapbs/modules/CHARMM/examples/datadir.def

                    INPUT STREAM SWITCHING TO UNIT    99
 RDTITL> * CHARMM TESTCASE DATA DIRECTORY ASSIGNMENT
 RDTITL> * $ID: DATADIR.DEF,V 1.2 2005/05/24 04:51:09 ROK EXP $
 RDTITL> FASTER ON
 Parameter: IN1 <- "" <empty>
  
 CHARMM>    faster on
 MISCOM> FAST option: EXPANDED (limited fast routines)
  
 CHARMM>    set 0 data/     ! input data directory
 Parameter: 0 <- "DATA/"
  
 CHARMM>    set 9 scratch/  ! scratch directory
 Parameter: 9 <- "SCRATCH/"
  
 CHARMM>    return
 VCLOSE: Closing unit   99 with status "KEEP"

                    RETURNING TO INPUT STREAM     5
  
 CHARMM>     
  
 CHARMM>    open read card unit 11 name @0top_all22_prot.inp
 Parameter: 0 -> "DATA/"
 VOPEN> Attempting to open::data/top_all22_prot.inp::
 OPNLGU> Unit 11 opened for READONLY access to /home/rok/Sandbox-100309/iapbs/modules/CHARMM/examples/data/top_all22_prot.inp
  
 CHARMM>    read rtf card unit 11
 MAINIO> Residue topology file being read from unit  11.
 TITLE> *>>>>>>>>CHARMM22 ALL-HYDROGEN TOPOLOGY FILE FOR PROTEINS <<<<<<
 TITLE> *>>>>>>>>>>>>>>>>>>>>> AUGUST 1999 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 TITLE> *>>>>>>> DIRECT COMMENTS TO ALEXANDER D. MACKERELL JR. <<<<<<<<<
 TITLE> *>>>>>> 410-706-7442 OR EMAIL: ALEX,MMIRIS.AB.UMD.EDU  <<<<<<<<<
 TITLE> *
  
 CHARMM>    close unit 11
 VCLOSE: Closing unit   11 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>    open read card unit 11 name @0par_all22_prot.inp
 Parameter: 0 -> "DATA/"
 VOPEN> Attempting to open::data/par_all22_prot.inp::
 OPNLGU> Unit 11 opened for READONLY access to /home/rok/Sandbox-100309/iapbs/modules/CHARMM/examples/data/par_all22_prot.inp
  
 CHARMM>    read para card unit 11

          PARAMETER FILE BEING READ FROM UNIT 11
 TITLE> *>>>> CHARMM22 ALL-HYDROGEN PARAMETER FILE FOR PROTEINS <<<<<<<<<<
 TITLE> *>>>>>>>>>>>>>>>>>>>>>> AUGUST 1999 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 TITLE> *>>>>>>> DIRECT COMMENTS TO ALEXANDER D. MACKERELL JR. <<<<<<<<<
 TITLE> *>>>>>> 410-706-7442 OR EMAIL: ALEX,MMIRIS.AB.UMD.EDU  <<<<<<<<<
 TITLE> *
 PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared.
  
 CHARMM>    close unit 11
 VCLOSE: Closing unit   11 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>    read sequence ALA 1
  
 CHARMM>    generate ALAD first ACE last CT3 setup warning
 THE PATCH 'ACE' WILL BE USED FOR THE FIRST RESIDUE
 THE PATCH 'CT3' WILL BE USED FOR THE LAST  RESIDUE
 ** WARNING ** BOND NOT FOUND FOR RESIDUE   1 ALA   .
 ATOMS "C     " "+N    " WERE REQUESTED.
 ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE   1 ALA   .
 ATOMS "N     " "-C    " "CA    " "HN    " WERE REQUESTED.
 ** WARNING ** IMPROPER NOT FOUND FOR RESIDUE   1 ALA   .
 ATOMS "C     " "CA    " "+N    " "O     " WERE REQUESTED.
 GENPSF> Segment   1 has been generated. Its identifier is ALAD.
 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
 PSFSUM> Summary of the structure file counters :
         Number of segments      =        1   Number of residues   =        1
         Number of atoms         =       22   Number of groups     =        6
         Number of bonds         =       21   Number of angles     =       36
         Number of dihedrals     =       42   Number of impropers  =        4
         Number of cross-terms   =        0
         Number of HB acceptors  =        2   Number of HB donors  =        2
         Number of NB exclusions =        0   Total charge =    0.00000
  
 CHARMM>     
  
 CHARMM>    read coor card
          SPATIAL COORDINATES BEING READ FROM UNIT  5
 RDTITL> * ALAD
 RDTITL> *
  
 CHARMM>     
  
 CHARMM>    coor orient

 ORIENT THE COORDINATES TO ALIGN WITH AXIS

 MOMENTS
     17.95397262     -8.67369571     19.57000165
                     58.09459225    -46.69084467
                                    111.17834589

 Transpose of the rotation matrix
     0.853685   -0.492562    0.169129
     0.475503    0.869659    0.132626
    -0.212411   -0.032800    0.976630
 CENTER OF ATOMS BEFORE TRANSLATION     1.48591     5.53196    -4.24329
 AXIS OF ROTATION IS  0.157009 -0.362127 -0.918810  ANGLE IS   31.79

 ALL COORDINATES ORIENTED IN THE MAIN SET BASED ON SELECTED ATOMS.

  
 CHARMM>     
  
 CHARMM>    PBEQ
 
   Calculations with the Poisson-Boltzmann Equation 
 
  
   PBEQ>    ! read in definition of radii
   PBEQ>      stream @0radius.str
 Parameter: 0 -> "DATA/"
 VOPEN> Attempting to open::data/radius.str::
 OPNLGU> Unit 99 opened for READONLY access to /home/rok/Sandbox-100309/iapbs/modules/CHARMM/examples/data/radius.str

                    INPUT STREAM SWITCHING TO UNIT    99
 RDTITL> * ATOMIC RADIUS DERIVED FROM SOLVENT ELECTROSTATIC CHARGE DISTRIBUTION
 RDTITL> * TESTED WITH FREE ENERGY PERTURBATION WITH EXPLICIT SOLVENT
 RDTITL> * AUTHORS:  MAFALDA NINA, DMITRII BELOGV, AND BENOIT ROUX
 RDTITL> * UNIVERSITY OF MONTREAL, JUNE 1996.
 RDTITL> * M. NINA AND B. ROUX. ATOMIC RADII FOR CONTINUUM ELECTROSTATICS CALCULATIONS BASED ON
 RDTITL> * MOLECULAR DYNAMICS FREE ENERGY SIMULATIONS. J. PHYS. CHEM. B 101: 5239-5248 (1997).
 RDTITL> *
 Parameter: IN1 <- "" <empty>
  
   PBEQ>     
  
   PBEQ>    ! UPDATES:
   PBEQ>    ! --------
   PBEQ>    !
   PBEQ>    ! GLU and ASP modified December 1st, 1998 by Mafalda Nina
   PBEQ>    !
   PBEQ>    ! Protonated histidine HSP has been included, January 1999 by Mafalda Nina
   PBEQ>    ! dG_elec = -68.15 kcal/mol (MD/FES) or -68.10 kcal/mol (PBEQ)
   PBEQ>    !
   PBEQ>    ! TEA and ions added by Benoit Roux, January 1999.
   PBEQ>    !
   PBEQ>    ! sodium added by Benoit Roux, November 2000
   PBEQ>     
  
   PBEQ>    ! Set to zero all H radii
   PBEQ>    scalar wmain set 0.0 sele chem H* end
 SELRPN>     12 atoms have been selected out of     22
  
   PBEQ>     
  
   PBEQ>    ! Set heavy atoms to average default values
   PBEQ>    scalar wmain set 2.3 sele chem C* end
 SELRPN>      6 atoms have been selected out of     22
  
   PBEQ>    scalar wmain set 1.8 sele chem O* end
 SELRPN>      2 atoms have been selected out of     22
  
   PBEQ>    scalar wmain set 2.3 sele chem N* end
 SELRPN>      2 atoms have been selected out of     22
  
   PBEQ>    scalar wmain set 2.3 sele chem S* end
 SELRPN>      0 atoms have been selected out of     22
  
   PBEQ>     
  
   PBEQ>    !Patches CT3 N-Methylamide C-terminus
   PBEQ>    !        ACE acetylated N-terminus (ACP for PRO)
   PBEQ>    scalar wmain set 2.06 sele (type CAY .or. type CAT) end
 SELRPN>      2 atoms have been selected out of     22
  
   PBEQ>    scalar wmain set 2.04 sele type CY end
 SELRPN>      1 atoms have been selected out of     22
  
   PBEQ>    scalar wmain set 1.52 sele type OY end
 SELRPN>      1 atoms have been selected out of     22
  
   PBEQ>    scalar wmain set 2.23 sele type NT end
 SELRPN>      1 atoms have been selected out of     22
  
   PBEQ>    scalar wmain set 1.40 sele type OT* end ! for COO- terminus
 SELRPN>      0 atoms have been selected out of     22
  
   PBEQ>     
  
   PBEQ>    !Backbone
   PBEQ>    scalar wmain set 2.04 sele type C  end
 SELRPN>      1 atoms have been selected out of     22
  
   PBEQ>           ! for peptide bond
  
   PBEQ>    scalar wmain set 1.52 sele type O  end
 SELRPN>      1 atoms have been selected out of     22
  
   PBEQ>           ! for peptide bond
  
   PBEQ>    scalar wmain set 2.23 sele type N  end
 SELRPN>      1 atoms have been selected out of     22
  
   PBEQ>           ! for peptide bond
  
   PBEQ>    scalar wmain set 2.86 sele type CA  end
 SELRPN>      1 atoms have been selected out of     22
  
   PBEQ>           ! for all CA except GLY
  
   PBEQ>    scalar wmain set 2.38 sele (resnam GLY .and. type CA) end
 SELRPN>      0 atoms have been selected out of     22
  
   PBEQ>           ! for GLY only
  
   PBEQ>     
  
   PBEQ>    !Hydrogens
   PBEQ>    scalar wmain set 0.00 sele type H* end
 SELRPN>     12 atoms have been selected out of     22
  
   PBEQ>           ! for all hydrogens
  
   PBEQ>     
  
   PBEQ>    !Carbons
   PBEQ>    scalar wmain set 2.67 sele type CB end
 SELRPN>      1 atoms have been selected out of     22
  
   PBEQ>           ! for all residues
  
   PBEQ>    scalar wmain set 2.46 sele type CG* end
 SELRPN>      0 atoms have been selected out of     22
  
   PBEQ>           ! for ARG, GLN, ILE, LYS, MET, PHE, THR, TRP, VAL, HSP, HSD
  
   PBEQ>    scalar wmain set 2.77 sele resnam GLU .and. type CG end
 SELRPN>      0 atoms have been selected out of     22
  
   PBEQ>           ! for GLU only
  
   PBEQ>    scalar wmain set 2.44 sele type CD* end
 SELRPN>      0 atoms have been selected out of     22
  
   PBEQ>           ! for ARG, ILE, LEU, LYS
  
   PBEQ>    scalar wmain set 1.98 sele (resnam GLN .and. type CD) .or. (resnam ASN .and. type CG) .or. -
   PBEQ>                               (resnam GLU .and. type CD) .or. (resnam ASP .and. type CG) end
 SELRPN>      0 atoms have been selected out of     22
  
   PBEQ>           ! for ASP, GLU, ASN, GLN
  
   PBEQ>    scalar wmain set 1.98 sele (resnam PRO .and. (type CB .or. type CG .or. type CD)) end
 SELRPN>      0 atoms have been selected out of     22
  
   PBEQ>           ! for PRO only
  
   PBEQ>    scalar wmain set 2.00 sele (resnam TYR .and. (type CE* .or. type CD* .or. -
   PBEQ>                              type CZ)) .or. (resnam PHE .and. (type CE* .or. -
   PBEQ>                              type CD* .or. type CZ))  end
 SELRPN>      0 atoms have been selected out of     22
  
   PBEQ>           ! for TYR, PHE rings
  
   PBEQ>    scalar wmain set 1.78 sele (resnam TRP .and. (type CE* .or. type CD* .or. -
   PBEQ>                              type CZ* .or. type CH2)) end
 SELRPN>      0 atoms have been selected out of     22
  
   PBEQ>           ! for TRP ring only
  
   PBEQ>    scalar wmain set 2.10 sele type CE end
 SELRPN>      0 atoms have been selected out of     22
  
   PBEQ>           ! for MET only
  
   PBEQ>    scalar wmain set 2.80 sele (resnam ARG .and. type CZ) .or. (resnam LYS .and. type CE) end
 SELRPN>      0 atoms have been selected out of     22
  
   PBEQ>           ! for ARG, LYS
  
   PBEQ>    scalar wmain set 1.98 select (( resnam HSD  .or. resnam HSP) .and. type CE1) -
   PBEQ>           .or. (( resnam HSD .or. resnam HSP)  .and. type CD2) end
 SELRPN>      0 atoms have been selected out of     22
  
   PBEQ>           ! for neutral HSD and protonated HSP
  
   PBEQ>     
  
   PBEQ>    !Oxygens
   PBEQ>    scalar wmain set 1.40 sele (resnam GLU .or. resnam ASP) .and. (type OE* .or. type OD*) end
 SELRPN>      0 atoms have been selected out of     22
  
   PBEQ>           ! for GLU, ASP
  
   PBEQ>    scalar wmain set 1.42 sele (resnam ASN .or. resnam GLN) .and. (type OE* .or. type OD*) end
 SELRPN>      0 atoms have been selected out of     22
  
   PBEQ>           ! for ASN, GLN
  
   PBEQ>    scalar wmain set 1.64 sele type OG* end
 SELRPN>      0 atoms have been selected out of     22
  
   PBEQ>           ! for SER, THR
  
   PBEQ>    scalar wmain set 1.85 sele (resnam TYR .and. type OH) end
 SELRPN>      0 atoms have been selected out of     22
  
   PBEQ>           ! for TYR only
  
   PBEQ>    scalar wmain set 2.2 select resname TIP3 .and. type OH2 end
 SELRPN>      0 atoms have been selected out of     22
  
   PBEQ>           ! for explicit water molecules
  
   PBEQ>     
  
   PBEQ>    !Nitrogens
   PBEQ>    scalar wmain set 1.80 sele resnam HSD  .and. (type NE2 .or. type ND1) end
 SELRPN>      0 atoms have been selected out of     22
  
   PBEQ>           ! for neutral HSD
  
   PBEQ>    scalar wmain set 2.30 sele resnam HSP  .and. (type NE2 .or. type ND1) end
 SELRPN>      0 atoms have been selected out of     22
  
   PBEQ>           ! for protonated HSP
  
   PBEQ>    scalar wmain set 2.13 sele resnam ARG .and. (type NH* .or. type NE) .or. -
   PBEQ>                          (resnam LYS .and. type NZ) end
 SELRPN>      0 atoms have been selected out of     22
  
   PBEQ>           ! for ARG, LYS
  
   PBEQ>    scalar wmain set 2.15 sele (resnam GLN .and. type NE2) .or. (resnam ASN .and. type ND2) end
 SELRPN>      0 atoms have been selected out of     22
  
   PBEQ>           ! for GLN, ASN
  
   PBEQ>    scalar wmain set 2.40 sele resnam TRP .and. type NE1 end
 SELRPN>      0 atoms have been selected out of     22
  
   PBEQ>           ! for TRP
  
   PBEQ>     
  
   PBEQ>    !Sulphur
   PBEQ>    scalar wmain set 2.00 sele type S* end
 SELRPN>      0 atoms have been selected out of     22
  
   PBEQ>           ! for MET, CYS
  
   PBEQ>     
  
   PBEQ>     
  
   PBEQ>    !Ions
   PBEQ>    scalar wmain set 2.035 select resname POT end
 SELRPN>      0 atoms have been selected out of     22
  
   PBEQ>           !potassium ion K+
  
   PBEQ>     
  
   PBEQ>    scalar wmain set 2.035 select resname CLA end
 SELRPN>      0 atoms have been selected out of     22
  
   PBEQ>           !chloride ion Cl-
  
   PBEQ>     
  
   PBEQ>    scalar wmain set 1.66 select resname SOD end
 SELRPN>      0 atoms have been selected out of     22
  
   PBEQ>           !sodium ion Na+
  
   PBEQ>     
  
   PBEQ>    scalar wmain set 2.15 sele resnam TEA .and. type N end
 SELRPN>      0 atoms have been selected out of     22
  
   PBEQ>    scalar wmain set 2.30 sele ( type C1 .or. type C2 .or. type C3 .or. type C4 ) .and. resnam TEA end
 SELRPN>      0 atoms have been selected out of     22
  
   PBEQ>    scalar wmain set 2.30 sele ( type C5 .or. type C6 .or. type C7 .or. type C8 ) .and. resnam TEA end
 SELRPN>      0 atoms have been selected out of     22
  
   PBEQ>           ! Tetramethylamonium (TEA)
  
   PBEQ>     
  
 VCLOSE: Closing unit   99 with status "KEEP"

                    RETURNING TO INPUT STREAM     5
  
   PBEQ>     
  
   PBEQ>    ! perform APBS calculation and write out DX files for elstat potential
   PBEQ>    ! charge and molecular surface
   PBEQ>      APBS mgmanual lpbe dimx 65 dimy 65 dimz 65 -
   PBEQ>      calcene 1 calcforce 0 debug 0 -
   PBEQ>      ionq1 1.0 ionc1 0.15 ionr1 2.0 ionq2 -1.0 ionc2 0.15 ionr2 2.0 -
   PBEQ>      gamma 0.2 -
   PBEQ>      wpot wsmol wchg wkappa wdiel -
   PBEQ>      sele all END

   PBEQ> Entering APBS module
 SELRPN>     22 atoms have been selected out of     22

   Calculation with     22 atoms
   APBS> Molecular dimensions:   11.157   7.449   6.090
  Writing potential to iapbs-pot.dx
  Writing charge distribution to iapbs-charge.dx
  Writing molecular accessibility to iapbs-smol.dx
  Writing kappa map to iapbs-kappa.dx
  Writing x-shifted dielectric map to iapbs-dielx.dx
  Writing y-shifted dielectric map to iapbs-diely.dx
  Writing z-shifted dielectric map to iapbs-dielz.dx
  
   PBEQ>    END
  
 CHARMM>     
  
 CHARMM>    ! elstat energy should be 249.441 kcal/mol
 CHARMM>    set elstatenergy = ?ENPB
 RDCMND substituted energy or value "?ENPB" to "218.329"
 Parameter: ELSTATENERGY <- "218.329"
  
 CHARMM>     
  
 CHARMM>    ! non-polar energy should be 18.3567 kcal/mol
 CHARMM>    set apolarenergy = ?ENNP
 RDCMND substituted energy or value "?ENNP" to "18.3567"
 Parameter: APOLARENERGY <- "18.3567"
  
 CHARMM>     
  
 CHARMM>     
  
 CHARMM>    stop
$$$$$$  New timer profile $$$$$
 Total time                      2.18 Other:            0.00

                    NORMAL TERMINATION BY NORMAL STOP
                    MAXIMUM STACK SPACE USED IS   47526
                    STACK CURRENTLY IN USE IS         0
                    NO WARNINGS WERE ISSUED
                    HEAP PRINTOUT-  HEAP SIZE   2048000
                    SPACE CURRENTLY IN USE IS         0
                    MAXIMUM SPACE USED IS          3718
                    FREE LIST
            PRINHP> ADDRESS:         1 LENGTH:   2048000 NEXT:         0

                    $$$$$ JOB ACCOUNTING INFORMATION $$$$$
                     ELAPSED TIME:     2.18  SECONDS 
                         CPU TIME:     2.18  SECONDS 
