Dear all,
I want to model a protein structure which has a
covalently linked LBT tag using xplor. The structures
of the protein and the tag are believed to be
unchanged but the linker(about 10 AAs) is flexible. A
structure after MD simulation was obtained without any
NMR constraints. Now we want to add RDCs and PCSs to
refine the model.
Since the structure of the protein and the tag are
known, we want to group them during the simulation but
not fix them. I know IVM (Dynamic Internal) is good
for dealing this kind of problem. And PCS will be
used so I modify the script downloaded from
Dr.Bertini's website. The problem is that the
structures generated by this script are identical.
Could you please help us check the script?
Here is the script I use:
evaluate ($init_t = 1000)
evaluate ($high_steps = 12000)
evaluate ($cool_steps = 6000)
parameter
@TOPPAR:parallhdg.pro
@par_axis_3.pro
@ion.param
end
structure
@1EU.psf
@axis_new_500.psf
end
coordinates @1EU4.pdb
coordinates @axis_xyzo_3_500.pdb
topology
@TOPPAR:topallhdg.pro
@ion.top
end
noe
nres=10000
class tensor
@tensors.tbl
class others
@metalcenter.tbl
end
flags exclude * include bonds angle impr vdw noe xpcs
xrdc xccr xang end
vector do (fbeta=10) (all)
vector do (mass=100) (all)
noe
ceiling=1000
averaging * cent
potential * soft
scale tensor 500.
scale others 50.
sqoffset * 0.0
sqconstant * 1.0
sqexponent * 2
soexponent * 1
asymptote * 0.1
rswitch * 0.5
end
xpcs
nres=2000
class EU
force 50.0
coeff 178.84 44.1
@pcshifts.tbl
end
!xrdc
! nres=2000
! class EU
! force 5.0
! coeff 4.58 2.85
! @rdcouplings.tbl
!end
parameter
nbonds
repel=1.
rexp=2 irexp=2 rcon=1.
nbxmod=3
wmin=0.01
cutnb=4.5 ctonnb=2.99 ctofnb=3.
tolerance=0.5
end
end
set abort off end
evaluate ($end_count=10)
coor copy end
evaluate ($count = 0)
while ($count < $end_count ) loop main
evaluate ($count=$count+1)
coor swap end
coor copy end
noe
potential * soft
end
{* ============================================
Initial minimization.*}
noe asymptote * 0.1 end
parameter nbonds repel=1. end end
!constraints fix=(resid 1:135 )
!end
minimize powell nstep=500 drop=10. nprint=25 end
{* =======================================
High-temperature dynamics.*}
! constraints fix=(resid 1:135 ) end
evaluate ($nstep1=int($high_steps * 2. / 3. ) )
evaluate ($nstep2=int($high_steps * 1. / 3. ) )
dynamics internal
nstep=$nstep1
timestep=0.004
group=( residue 1:130)
group=( residue 145:154 )
group=( residue 170)
group=( residue 500)
! group=( residue 20:22 ) group=( residue 23:30 )
! dynmode=tcou
hinge=full (resid 1:130)
itype= powell
tbath=$init_t
nprint=25
ntrfrq=1
end
!dynamics verlet
! nstep=$nstep1 timestep=0.005 iasvel=maxwell
firstt=$init_t
! tcoupling=true tbath=$init_t nprint=50 iprfrq=0
! end
{* ============= Tilt the asymptote and increase
weights on geometry.*}
noe asymptote * 1.0 end
! constraints fix=(resid 1:135) end
dynamics internal
nstep=$nstep2
timestep=0.004
group=(residue 1:130)
group=( residue 145:154 )
group=( residue 170)
group=(residue 500)
! group=( residue 20:22 ) group=( residue 23:30 )
! dynmode=tcou
hinge=full (resid 1:130)
itype= powell
tbath=$init_t
nprint=25
ntrfrq=1
end
! dynamics verlet
! nstep=$nstep2 timestep=0.005 iasvel=current
tcoupling=true
! tbath=$init_t nprint=50 iprfrq=0
! end
{* ================================================
Cool the system.*}
evaluate ($final_t = 100) { K }
evaluate ($tempstep = 50) { K }
evaluate ($ncycle = ($init_t-$final_t)/$tempstep)
evaluate ($nstep = int($cool_steps/$ncycle))
evaluate ($ini_rad = 0.9) evaluate
($fin_rad = 0.75)
evaluate ($ini_con= 0.003) evaluate
($fin_con= 4.0)
evaluate ($bath = $init_t)
evaluate ($k_vdw = $ini_con)
evaluate ($k_vdwfact =
($fin_con/$ini_con)^(1/$ncycle))
evaluate ($radius= $ini_rad)
evaluate ($radfact =
($fin_rad/$ini_rad)^(1/$ncycle))
evaluate ($i_cool = 0)
while ($i_cool < $ncycle) loop cool
evaluate ($i_cool=$i_cool+1)
evaluate ($bath = $bath - $tempstep)
evaluate ($k_vdw=min($fin_con,$k_vdw*$k_vdwfact))
evaluate ($radius=max($fin_rad,$radius*$radfact))
parameter nbonds repel=$radius end end
dynamics internal
nstep=$nstep
timestep=0.004
group=(residue 1:130)
group=( residue 145:154 )
group=(residue 170)
group=(residue 500)
! group=( residue 20:22 ) group=( residue 23:30 )
! dynmode=tcou
hinge=full (resid 1:130)
itype=powell
tbath=$bath
nprint=25
ntrfrq=1
end
! constraints fix=(resid 1:135) end
! dynamics verlet
! nstep=$nstep time=0.005 iasvel=current
firstt=$bath
! tcoup=true tbath=$bath nprint=$nstep iprfrq=0
! end
{===============================================>}
{*Abort condition.*}
evaluate ($critical=$temp/$bath)
if ($critical > 10. ) then
display ****&&&& rerun job with smaller
timestep (i.e., 0.003)
remark stop
end if
end loop cool
{* ==============================================
Final minimization.*}
!constraints fix=( resid 1:135) end
noe
potential * square
end
minimize powell nstep=2000 drop=10.0 nprint=100 end
{* ================================ Write out the
final structure(s).*}
print threshold=0.5 noe
evaluate ($rms_noe=$result)
evaluate ($violations_noe=$violations)
xpcs print threshold 0.15 all end
evaluate ($rms_xpcs=$result)
evaluate ($violations_xpcs=$violations)
xrdc print threshold 0.10 all end
evaluate ($rms_xrdc=$result)
evaluate ($violations_xrdc=$violations)
xccr print threshold 0.20 all end
evaluate ($rms_xccr=$result)
evaluate ($violations_xccr=$violations)
xang print threshold 0.20 all end
evaluate ($rms_xang=$result)
evaluate ($violations_xang=$violations)
print thres=0.05 bonds
evaluate ($rms_bonds=$result)
print thres=5. angles
evaluate ($rms_angles=$result)
print thres=5. impropers
evaluate ($rms_impropers=$result)
remarks
============================================================
remarks
overall,bonds,angles,improper,vdw,noe
remarks energies: $ener, $bond, $angl, $impr, $vdw,
$noe
remarks
remarks xpcs,xrdc,xccr,xang
remarks energies: $xpcs, $xrdc, $xccr, $xang
remarks
============================================================
remarks bonds,angles,impropers,noe
remarks rms-d:
$rms_bonds,$rms_angles,$rms_impropers,$rms_noe
remarks
remarks xpcs,xrdc,xccr,xang
remarks rms-d:
$rms_xpcs,$rms_xrdc,$rms_xccr,$rms_xang
remarks
============================================================
remarks noe
remarks violations.: $violations_noe
remarks
remarks
remarks xpcs,xrdc,xccr
remarks violations.:
$violations_xpcs,$violations_xrdc,$violations_xccr
remarks xang
remarks violations.: $violations_xang
remarks
============================================================
{======================>} {*Name(s) of the family of
final structures.*}
evaluate ($filename="sa_"+encode($count)+".pdb")
write coordinates output =$filename end
end loop main
remark stop
Any help will be great appreciated.
Thanks
Tiandi
___________________________________________________________
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http://mail.yahoo.com.cn/
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