Reordering of atoms in Generate..
Mark Roe
roe at biochemistry.ucl.ac.uk
Fri Apr 3 04:30:24 EST 1998
Hi All,
I am trying to run NCS restraints in X-PLOR 3.851. However when I generate
my DNA strands, the first always has some atoms reordered in every base in
the strand in the output pdb file. Thus the NCS fails because the atoms
are not serially identical. I have never seen this problem with protein
files, so I presume my DNA setup is not correct?
Does anyone know why generate does this and how to avoid it?
(generate.inp file is at the bottom of this message.)
Cheers,
Mark Roe.
Dr. S. M. Roe,
LICR/UCL X-ray Crystallography Laboratory,
Department of Biochemistry,
University College London,
Gower Street,
London.
WC1E 6BT.
Tel. (44) 171 504 2303
Fax. (44) 171 380 7193
E-mail roe at biochem.ucl.ac.uk
____________________________________________________________________________
____________________________________________________________________________
remarks file generate/generate.inp
remarks Generate structure file and hydrogens for a protein
topology @TOPPAR:tophcsdx.pro
@TOPPAR:dna-rna.top
end {*Read topology file.*}
parameter
@TOPPAR:protein_rep.param {*Read empirical potential*}
@TOPPAR:dna-rna_rep.param {*parameter file CHARMM19 *}
{*with modifications. *}
end
segment {*Generate protein.*}
name="AAAA"
chain
LINK NUC HEAD - * TAIL + * END
FIRST 5TER TAIL + * END {* phosphorylated 5' end *}
LAST 3TER HEAD - * END
coordinates @test_aaaa.pdb {*interpret coordinate file to*}
end {*obtain the sequence. *}
end
for $1 in ( 1 2 3 4 5 6 7 8 ) loop main
patch deox reference=nil=( resid $1 ) end
end loop main
coordinates @test_aaaa.pdb {*Here we actually read the*}
{*coordinates. *}
segment {*Generate protein.*}
name="AAAB"
chain
LINK NUC HEAD - * TAIL + * END
FIRST 5TER TAIL + * END {* phosphorylated 5' end *}
LAST 3TER HEAD - * END
coordinates @test_aaab.pdb {*interpret coordinate file to*}
end {*obtain the sequence. *}
end
for $1 in ( 1 2 3 4 5 6 7 8 ) loop main
patch deox reference=nil=( resid $1 ) end
end loop main
coordinates @test_aaab.pdb {*Here we actually read the*}
{*coordinates. *}
segment {*Generate protein.*}
name="AAAC"
chain
LINK NUC HEAD - * TAIL + * END
FIRST 5TER TAIL + * END {* phosphorylated 5' end *}
LAST 3TER HEAD - * END
coordinates @test_aaac.pdb {*interpret coordinate file to*}
end {*obtain the sequence. *}
end
for $1 in ( 1 2 3 4 5 6 7 8 ) loop main
patch deox reference=nil=( resid $1 ) end
end loop main
coordinates @test_aaac.pdb {*Here we actually read the*}
{*coordinates. *}
segment {*Generate protein.*}
name="AAAD"
chain
LINK NUC HEAD - * TAIL + * END
FIRST 5TER TAIL + * END {* phosphorylated 5' end *}
LAST 3TER HEAD - * END
coordinates @test_aaad.pdb {*interpret coordinate file to*}
end {*obtain the sequence. *}
end
for $1 in ( 1 2 3 4 5 6 7 8 ) loop main
patch deox reference=nil=( resid $1 ) end
end loop main
coordinates @test_aaad.pdb {*Here we actually read the*}
{*coordinates. *}
segment {*Generate protein.*}
name="AAAE"
chain
LINK NUC HEAD - * TAIL + * END
FIRST 5TER TAIL + * END {* phosphorylated 5' end *}
LAST 3TER HEAD - * END
coordinates @test_aaae.pdb {*interpret coordinate file to*}
end {*obtain the sequence. *}
end
for $1 in ( 1 2 3 4 5 6 7 8 ) loop main
patch deox reference=nil=( resid $1 ) end
end loop main
coordinates @test_aaae.pdb {*Here we actually read the*}
{*coordinates. *}
segment {*Generate protein.*}
name="AAAF"
chain
LINK NUC HEAD - * TAIL + * END
FIRST 5TER TAIL + * END {* phosphorylated 5' end *}
LAST 3TER HEAD - * END
coordinates @test_aaaf.pdb {*interpret coordinate file to*}
end {*obtain the sequence. *}
end
for $1 in ( 1 2 3 4 5 6 7 8 ) loop main
patch deox reference=nil=( resid $1 ) end
end loop main
coordinates @test_aaaf.pdb {*Here we actually read the*}
{*coordinates. *}
segment {*Generate protein.*}
name="AAAG"
chain
LINK NUC HEAD - * TAIL + * END
FIRST 5TER TAIL + * END {* phosphorylated 5' end *}
LAST 3TER HEAD - * END
coordinates @test_aaag.pdb {*interpret coordinate file to*}
end {*obtain the sequence. *}
end
for $1 in ( 1 2 3 4 5 6 7 8 ) loop main
patch deox reference=nil=( resid $1 ) end
end loop main
coordinates @test_aaag.pdb {*Here we actually read the*}
{*coordinates. *}
segment {*Generate protein.*}
name="AAAH"
chain
LINK NUC HEAD - * TAIL + * END
FIRST 5TER TAIL + * END {* phosphorylated 5' end *}
LAST 3TER HEAD - * END
coordinates @test_aaah.pdb {*interpret coordinate file to*}
end {*obtain the sequence. *}
end
for $1 in ( 1 2 3 4 5 6 7 8 ) loop main
patch deox reference=nil=( resid $1 ) end
end loop main
coordinates @test_aaah.pdb {*Here we actually read the*}
{*coordinates. *}
{===>} {set hydrogen flag: must be TRUE for NMR, atomic resolution X-ray }
{ crystallography or modelling. Set the FALSE for most X-ray }
{ crystallographic applications at resolution > 1. A }
evaluate ($hydrogen_flag=TRUE)
if ($hydrogen_flag=TRUE) then
flags exclude vdw elec end {*Do QUICK hydrogen building w/o*}
{*vdw and elec terms. *}
hbuild {*This statement builds *}
selection=( hydrogen and not known) {*missing hydrogens, which are*}
phistep=45 {*needed for the force field. *}
end
constraints fix=( not hydrogen ) end {* Minimize hydrogen positions. *}
flags include vdw end
minimize powell
nstep=40
end
constraints fix=( not all ) end
else
delete selection=( hydrogen ) end
end if
{===>}
{* Set occupancies and b-factors if necessary *}
{ vector do (q=1.0 ) ( attribute q # 1.0 ) }
vector do (b=80.) ( attribute b > 80. )
vector do (b=10.) ( attribute b < 10. )
{===>}
write coordinates output=junk.pdb end {*Write out coordinates.*}
{===>}
write structure output=junk.psf end {*Write out structure file.*}
stop
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