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In this example, we search over the conformational space of residues 127 to 131 in flavodoxin. The search is done using backbone degrees of freedom over residue 127 and 128, with a chain closure over residues 129 to 131. We do searches to find both the minimum energy conformation and minimum RMS deviation to the X-ray crystal structure.
Construction of helix segment 127-131 in flavodoxin.
In this run, we find both the theoretical lower limit and the
lowest energy conformations.
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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
READ PSF FILE UNIT 10
OPEN UNIT 11 NAME CGTD:FLVDOX.MOD UNFORM READ
READ COOR FILE UNIT 11
COOR COPY COMP
OPEN UNIT 60 NAME 127FLVRMS.CG UNFORM WRITE ! Conformation file
OPEN UNIT 70 NAME CGDATA:TOPCGEN2.INP FORM READ ! Sidechain topology
OPEN UNIT 51 NAME CGDATA:EMAPGLY30.OMP FORM READ ! Glycine torsion map
OPEN UNIT 52 NAME CGDATA:EMAPALA30.OMP FORM READ ! Alanine torsion map
OPEN UNIT 53 NAME CGDATA:EMAPPRO30.OMP FORM READ ! Proline torsion map
OPEN UNIT 55 NAME CGDATA:PRO.CNS FORM READ ! Proline constructor
OPEN UNIT 40 NAME 127FLV.STS FORM WRITE ! Status file
!
! Run the search now.
!
CGEN -
STATUS SETPRN UNIT 40 END -
HBCG CUTHB 4.5 CUTHBA 90.0 -
CTONHA 98.0 CTOFHA 99.0 CTONHB 98.0 CTOFHB 99.0 END -
- ! Evaluate energy using constant dielectric of 50, distance cutoff = 5 A
NBCG CUTNB 5.0 ATOM CTONNB 98.0 CTOFNB 99.0 END -
- !
- ! The following Backbone degree of freedom contains CLSA optimizations to
- ! the correct terminators for the search.
- !
BACK MAXEVDW 20 STARTRES 1 127 LASTRES 1 128 CISTRANS CLSA 1 131 CA $ -
CHAIN STARTRES 1 129 CISTRANS MAXEVDW 20 $ -
SIDE SGRID MIN STARTRES 1 127 LASTRES 1 131 -
SIDEOPT INDE MAXEVDW 20 EVAL RMS $ -
- !
- ! We compare RMS's to the starting coordinates
- !
EVL RMS $ -
WRITE CUNIT 60 $ -
GLYMAP 51 ALAMAP 52 PROMAP 53 PROCONS 55 -
GLYEMAX 2 ALAEMAX 2 PROEMAX 2 STUNIT 70 -
ERINGPRO 50 -
! The following contains the title used in the conformation file
127FLVRMS.CG
Conformations of helix segment 127-131 in flavodoxin.
RMS driven.
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COOR COPY ! Restore original coordinates.
OPEN UNIT 60 NAME 127FLVE.CG UNFORM WRITE ! Conformation file
OPEN UNIT 70 NAME CGDATA:TOPCGEN2.INP FORM READ ! Sidechain topology
OPEN UNIT 51 NAME CGDATA:EMAPGLY30.OMP FORM READ ! Glycine torsion map
OPEN UNIT 52 NAME CGDATA:EMAPALA30.OMP FORM READ ! Alanine torsion map
OPEN UNIT 53 NAME CGDATA:EMAPPRO30.OMP FORM READ ! Proline torsion map
OPEN UNIT 55 NAME CGDATA:PRO.CNS FORM READ ! Proline constructor
OPEN UNIT 40 NAME 127FLV.STS FORM WRITE ! Status file
!
! Run the search now.
!
CGEN -
STATUS SETPRN UNIT 40 END -
HBCG CUTHB 4.5 CUTHBA 90.0 -
CTONHA 98.0 CTOFHA 99.0 CTONHB 98.0 CTOFHB 99.0 END -
- ! Evaluate energy using constant dielectric of 50, distance cutoff = 5 A
NBCG CUTNB 5.0 ATOM CTONNB 98.0 CTOFNB 99.0 END -
- !
- ! The following Backbone degree of freedom contains CLSA optimizations to
- ! the correct terminators for the search.
- !
BACK MAXEVDW 20 STARTRES 1 127 LASTRES 1 128 CISTRANS CLSA 1 131 CA $ -
CHAIN STARTRES 1 129 CISTRANS MAXEVDW 20 $ -
SIDE SGRID MIN STARTRES 1 127 LASTRES 1 131 -
SIDEOPT ITER MAXEVDW 20 EVAL E $ -
- !
- ! We do a simple energy evaluation for the five residues. The
- ! energies will be written to the conformation file.
- !
EVL MINI ENERGY END $ -
WRITE CUNIT 60 $ -
GLYMAP 51 ALAMAP 52 PROMAP 53 PROCONS 55 -
GLYEMAX 2 ALAEMAX 2 PROEMAX 2 STUNIT 70 -
ERINGPRO 50 -
! The following contains the title used in the conformation file
127FLVE.CG
Conformations of helix segment 127-131 in flavodoxin.
Energy calculations.
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