Calculating molecular properties

Top level: CHARMM

This script can be used as a template to compute properties of a molecule. Here, it reads in the crd and psf file generate above for alanine dipeptide and computes the energy of the conformation in the crd file.

bomblev -2

set molname aladipeptide 

! SET PATH to topology and parameter files 
! quotes MUST if path has both upper and lower case letters    
set pardir "/home/ss2029/svn/CHARMM31/toppar"

! READ TOPOLOGY 
open unit 1 read formatted name @pardir/"top_all22_prot.inp"
read rtf card unit 1
close unit 1

! READ PARAMS 
open unit 2 read formatted name @pardir/"par_all22_prot.inp"
read para card unit 2
close unit 2

! READ psf from file 
open unit 1 form read name @molname.psf
read psf card unit 1
close unit 1

! READ coord from file 
open unit 1 card read name @molname.crd
read coor card unit 1 
close unit 1

! COMPUTE ENERGY 
UPDATE NBOND atom switch cdie vdw vswitch -
   ctonnb 979 ctofnb 989 cutnb 999

ENERgy 

! end of file 

Running as

$ ~/svn/CHARMM31/exec/gnu/charmm  < ener.inp

gives the output

  :
  :
 CHARMM>    ENERgy

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    CDIElec  SWITch   VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  =999.000 CTEXNB =999.000 CTONNB =979.000 CTOFNB =989.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  1.000 EPS    =  1.000
 NBXMOD =      5
 There are      174 atom  pairs and       98 atom  exclusions.
 There are        0 group pairs and       11 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 == PRIMARY == SPACE FOR      221 ATOM PAIRS AND        0 GROUP PAIRS

 General atom nonbond list generation found:
      174 ATOM PAIRS WERE FOUND FOR ATOM LIST
        0 GROUP PAIRS REQUIRED ATOM SEARCHES

ENER ENR:  Eval#     ENERgy      Delta-E         GRMS
ENER INTERN:          BONDs       ANGLes       UREY-b    DIHEdrals    IMPRopers
ENER EXTERN:        VDWaals         ELEC       HBONds          ASP         USER
 ----------       ---------    ---------    ---------    ---------    ---------
ENER>        0     70.55732      0.00000     43.03708
ENER INTERN>        0.02020     28.80010      0.11396     10.08902     51.30174
ENER EXTERN>        5.47894    -25.24663      0.00000      0.00000      0.00000
 ----------       ---------    ---------    ---------    ---------    ---------
  
 CHARMM>     
  
$$$$$$  New timer profile $$$$$
   List time               0.00959 Other:    0.00000
         Electrostatic & VDW     0.00004 Other:    0.00000
      Nonbond force           0.01572 Other:    0.01568
         Bond energy             0.00093 Other:    0.00000
         Angle energy            0.00004 Other:    0.00000
         Dihedral energy         0.00003 Other:    0.00000
         Restraints energy       0.00000 Other:    0.00000
      INTRNL energy           0.01781 Other:    0.01682
   Energy time             0.04364 Other:    0.01010
 Total time              0.43943 Other:    0.38620

                    NORMAL TERMINATION BY END OF FILE
                    MAXIMUM STACK SPACE USED IS   47526
                    STACK CURRENTLY IN USE IS         0
                    MOST SEVERE WARNING WAS AT LEVEL  1
                    HEAP PRINTOUT-  HEAP SIZE   2048000
                    SPACE CURRENTLY IN USE IS       172
                    MAXIMUM SPACE USED IS          2008
                    FREE LIST
            PRINHP> ADDRESS:         1 LENGTH:   2047828 NEXT:         0

                    $$$$$ JOB ACCOUNTING INFORMATION $$$$$
                     ELAPSED TIME:     0.44  SECONDS 
                         CPU TIME:     0.00  SECONDS 
FORTRAN STOP
 

Top level: CHARMM