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This example illustrates how every sidechain in a structure can be reconstructed. This run serves as an important test of CONGEN. Note that cysteines would not rebridged correctly because the CONGEN command doesn't handle the disulphides at present.
Reconstructing side chains on flavodoxin backbones
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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
OPEN UNIT 11 NAME CGTD:FLVDOX.MOD UNFORM READ
READ PSF FILE UNIT 10
READ COOR FILE UNIT 11
COOR COPY COMP
ENERGY
OPEN UNIT 70 NAME CGDATA:TOPCGEN3.INP FORM READ
!
! The map and proline constructor files are required for all CONGEN
! runs even if they are not used.
!
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
CONGEN -
SIDE VAVOID MAXEVDW 20 -
SIDEOPT ITER EVAL E MAXSIDE 30 -
SGRID MIN -
STARTRES 1 1 LASTRES 1 138 $ -
EVL MINI ENERGY END $ -
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
Conformations of sidechains in flavodoxin model
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!
! Compare sidechain coordinates
!
COOR RMS CLEAR ATOM * * NT ATOM * * N ATOM * * CA ATOM * * C ATOM * * CB -
ATOM * * O ATOM * * OT1 ATOM * * OT2 ATOM * * H -
ATOM * NTER * ATOM * 1 HT3 NOT
OPEN UNIT 21 NAME FLVDOXS.MOD WRITE UNFORM
WRITE COOR FILE UNIT 21
FLVDOXS.MOD
Sequentially constructed flavodoxin. Side chains generated by CONGEN.
SGRID 30 SGRID 60 for ARG and LYS.
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ANAL
SET LINESZ 80
COMPARE COOR COMP $
BUILD DIFF ATOM R
DELETE VALUE ABS LT 0.0005 $ ! Delete backbone comparisons
ADD STATS RMS $ PLACE RESIDUE SEGMENT $ ! Add residue statistics
PRINT TABLE PRETTY
END