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This example is taken from $CGT/cgpbe2.inp. It illustrates using the substitution of the Poisson-Boltzmann electrostatic energy for the Coulomb energy for evaluating all the conformers generated by search, where the sidechains are optimized using the CHARMM potential. This is necessary to keep the execution time reasonable, but this is not a good example for a real application.
Conformational search over NEW
Test of PBE evaluation in parallel
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OPEN NAME CGDATA:RTOPH8.MOD UNIT 01 READ UNFORM
OPEN NAME CGDATA:PARAM5.MOD UNIT 03 READ UNFORM
OPEN NAME CGTD:newpsf.mod UNIT 12 READ UNFORM
OPEN NAME CGTD:NEWV.MOD UNIT 14 READ UNFORM
READ RTF UNIT 1
READ PARAMETER UNIT 3
READ PSF FILE UNIT 12
READ COOR FILE UNIT 14
parallel loops ncpu 4
!
! Setup the conditions for using Poisson-Boltzmann equation.
! The grid size is too large for a real calculation, though.
!
PBE SETUP IONSTR 0.15 BOUNDARY SDEBYE CENTER SOLVENT 78 GRID 1.5 -
WATER 0.0 STERN 2.0 XDIM 50 YDIM 50 ZDIM 50 -
TRILINEAR INTERIOR 2.0 ALL END
PBE POTENTIAL RTOLER 1.0E-3 MAXITER 1000
PBE ENERGY
!
! Generate conformations for the loop H 31-35 using the CHARMM
! potential energy.
!
OPEN UNIT 60 NAME CGPBE2.CG1 UNFORM WRITE
OPEN UNIT 70 NAME CGDATA:TOPCGEN2.INP FORM READ
OPEN UNIT 51 NAME CGDATA:EMAPGLY30.OMP FORM READ
OPEN UNIT 52 NAME CGDATA:EMAPALA30.OMP FORM READ
OPEN UNIT 53 NAME CGDATA:EMAPPRO30.OMP FORM READ
OPEN UNIT 55 NAME CGDATA:PRO.CNS FORM READ
CGEN -
SEARCH DEPTH END -
NBCG CUTNB 5.0 CTONNB 98.0 CTOFNB 99.0 END -
HBCG CUTHB 4.5 CTONHB 98.0 CTOFHB 99.0 -
CUTHBA 90.0 CTONHA 90.0 CTOFHA 90.0 END -
BACK CISTRANS STARTRES H 31 LASTRES H 32 MAXEVDW 100 CLSA H 35 CA $ -
CHAIN CISTRANS STARTRES H 33 MAXEVDW 100 $ -
SIDE STARTRES H 31 LASTRES H 35 MAXEVDW 100 SIDEOPT ITER SGRID MIN EVAL E $ -
WRITE CUNIT 60 $ -
ERINGPRO 50 GLYMAP 51 ALAMAP 52 PROMAP 53 PROCONS 55 -
GLYEMAX 2 ALAEMAX 2 PROEMAX 2 STUNIT 70
CGPBE2.CG1
CGPBE2 test case
Conformations of H1 loop in NEW.
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!
! Now evaluate the conformations using the Poisson-Boltzmann energy
! substituting for the Coulomb energy.
!
CLOSE UNIT 60
OPEN UNIT 59 NAME CGPBE2.CG1 UNFORM READ
OPEN UNIT 60 NAME CGPBE2.CG UNFORM WRITE
OPEN UNIT 70 NAME CGDATA:TOPCGEN2.INP FORM READ
OPEN UNIT 51 NAME CGDATA:EMAPGLY30.OMP FORM READ
OPEN UNIT 52 NAME CGDATA:EMAPALA30.OMP FORM READ
OPEN UNIT 53 NAME CGDATA:EMAPPRO30.OMP FORM READ
OPEN UNIT 55 NAME CGDATA:PRO.CNS FORM READ
CGEN -
PBE NEWB END -
SEARCH DEPTH END -
NBCG CUTNB 5.0 CTONNB 98.0 CTOFNB 99.0 END -
HBCG CUTHB 4.5 CTONHB 98.0 CTOFHB 99.0 -
CUTHBA 90.0 CTONHA 90.0 CTOFHA 90.0 END -
RBEST UNIT 59 NBEST 9999 $ -
EVL MINI ENERGY END $ -
WRITE CUNIT 60 $ -
ERINGPRO 50 GLYMAP 51 ALAMAP 52 PROMAP 53 PROCONS 55 -
GLYEMAX 2 ALAEMAX 2 PROEMAX 2 STUNIT 70
CGPBE2.CG
CGPBE2 test case
Conformations of H1 loop in NEW.
*
!
! Extract the best conformation
!
OPEN UNIT 60 NAME CGPBE2.CG READ UNFORM
XCONF 60 BEST 1