This example illustrates how a energy directed search can be executed where the search is driven by the energies of complete residues along the loop. Note that we reconstruct sidechains repeatedly in order to get an accurate energy.
Energy directed conformational search
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!
! Open and read RTF, parameters, PSF, and coordinates.
!
OPEN NAME CGDATA:RTOPH8.MOD UNIT 01 READ UNFORM
READ RTF UNIT 1
OPEN NAME CGDATA:PARAM5.MOD UNIT 03 READ UNFORM
READ PARAMETER UNIT 3
OPEN UNIT 10 NAME CGTD:FLVDOXPSF.MOD UNFORM READ
OPEN UNIT 11 NAME CGTD:FLVDOX.MOD UNFORM READ
READ PSF FILE UNIT 10
READ COOR FILE UNIT 11
ENERGY
!
! Open files needed for the search
!
OPEN UNIT 60 NAME EXAMPLE.CG UNFORM WRITE
OPEN UNIT 70 NAME CGDATA:TOPCGEN3.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
OPEN UNIT 40 NAME EXAMPLE.STS FORM WRITE
PARALLEL ! Setup a parallel search
CONGEN -
SEARCH EVAL ENERGY END -
- ! Allocate a big tree so many branches can be explored.
TREE LIMIT 1000000 TOPSAVE 4 REDUCTION 2.0 SDSAVE 0.0 PRTFRQ 1000000 END -
- ! Write a status file so we can get see the progress.
STATUS UNIT 40 END -
- ! The CHECKPOINT option is used to set the frequency of status file updates.
CHECKPOINT NODE 1000000 TIME 120 UNIT -1 END -
- !
- ! Build the loop from each end toward the middle
- ! Force the program to expand all backbone and chain closure open nodes
- ! so that only complete residues will be used to direct the search process.
-
BACK EIMMED STARTRES 1 38 MAXEVDW 20.0 CISTRANS CLSA 1 48 CA $ -
SIDE VAVOID MAXEVDW 5.0 SIDEOPT ITER EVAL E MAXSIDE 30 SGRID MIN -
STARTRES 1 38 $ -
BACK EIMMED STARTRES 1 48 MAXEVDW 20.0 CISTRANS CLSA 1 39 N REVERSE $ -
SIDE VAVOID MAXEVDW 5.0 SIDEOPT ITER EVAL E MAXSIDE 30 SGRID MIN -
STARTRES 1 38 -
STARTRES 1 48 $ -
BACK EIMMED STARTRES 1 39 MAXEVDW 20.0 CISTRANS CLSA 1 47 CA $ -
SIDE VAVOID MAXEVDW 5.0 SIDEOPT ITER EVAL E MAXSIDE 30 SGRID MIN -
STARTRES 1 38 LASTRES 1 39 -
STARTRES 1 48 $ -
BACK EIMMED STARTRES 1 47 MAXEVDW 20.0 CISTRANS CLSA 1 40 N REVERSE $ -
SIDE VAVOID MAXEVDW 5.0 SIDEOPT ITER EVAL E MAXSIDE 30 SGRID MIN -
STARTRES 1 38 LASTRES 1 39 -
STARTRES 1 47 LASTRES 1 48 $ -
BACK EIMMED STARTRES 1 40 MAXEVDW 20.0 CISTRANS CLSA 1 46 CA $ -
SIDE VAVOID MAXEVDW 5.0 SIDEOPT ITER EVAL E MAXSIDE 30 SGRID MIN -
STARTRES 1 38 LASTRES 1 40 -
STARTRES 1 47 LASTRES 1 48 $ -
BACK EIMMED STARTRES 1 46 MAXEVDW 20.0 CISTRANS CLSA 1 41 N REVERSE $ -
SIDE VAVOID MAXEVDW 5.0 SIDEOPT ITER EVAL E MAXSIDE 30 SGRID MIN -
STARTRES 1 38 LASTRES 1 40 -
STARTRES 1 46 LASTRES 1 48 $ -
BACK EIMMED STARTRES 1 41 MAXEVDW 20.0 CISTRANS CLSA 1 45 CA $ -
SIDE VAVOID MAXEVDW 5.0 SIDEOPT ITER EVAL E MAXSIDE 30 SGRID MIN -
STARTRES 1 38 LASTRES 1 41 -
STARTRES 1 46 LASTRES 1 48 $ -
BACK EIMMED STARTRES 1 45 MAXEVDW 20.0 CISTRANS CLSA 1 42 N REVERSE $ -
SIDE VAVOID MAXEVDW 5.0 SIDEOPT ITER EVAL E MAXSIDE 30 SGRID MIN -
STARTRES 1 38 LASTRES 1 41 -
STARTRES 1 45 LASTRES 1 48 $ -
CHAIN EIMMED STARTRES 1 42 CISTRANS MAXEVDW 20.0 $ -
SIDE VAVOID MAXEVDW 5.0 SIDEOPT ITER EVAL E MAXSIDE 30 SGRID MIN -
STARTRES 1 38 LASTRES 1 48 $ -
EVL MINI ENERGY END $ -
WRITE CUNIT 60 MINCUT 3 $ -
GLYMAP 51 ALAMAP 52 PROMAP 53 PROCONS 55 -
GLYEMAX 2 ALAEMAX 2 PROEMAX 2 STUNIT 70 -
ERINGPRO 50 -
HBCG CUTHB 4.5 CUTHBA 90 CTONHB 98 CTOFHB 99 CTONHA 98 CTOFHA 99 END -
NBCG CUTNB 8.0 ATOM CTONNB 98.0 CTOFNB 99.0 END
Directed search example.
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!
! Now extract the best conformation
!
CLOSE UNIT 60
OPEN UNIT 60 NAME EXAMPLE.CG UNFORM READ
XCONF 60 BEST 1