[Xplor-nih] annealing with ambiguous restraints
Leao Lagarto
dodgy_spin at yahoo.co.uk
Wed Jul 11 09:20:06 EDT 2007
Dear XPLOR-NIH community
I would like to request some help dealing with
simulated annealing protocol (sa.inp). As input in the
sa.inp file I write my topology, my template pdb file,
and the restraints: dihedral and noe (unambiguous
only!). However when I calculated my 100 structures
for futher water refinement I got an error message
%NOESET-ERR: error in selection - no atoms spec.
%NOE-ERR: problem at 1588 -999.000 -999.000
-999.000 -999.000
As a result the pdb files bring 2 violations
REMARK cdih end_coup end_coup_gly noe
REMARK violations : 2 2
the program doesn't crash but I believe that is not
good signal to get ERR in the outputs files :-)
In my opinion the problem should be in my xplor script
(sa.inp -please see below) dealing with the ambiguous
restraints or in the *.tbl file.
So if anybody has a suggestion please let me know.
! set the weights for the experimental energy terms
evaluate ($knoe = 50.0) ! noes
evaluate ($asym = 0.1) ! slope of NOE potential
evaluate ($kcdi = 10.0) ! torsion angles
evaluate ($kandb = 0.001)
evaluate ($kimdb = 0.001)
evaluate ($k_ncs = 0.01)
!evaluate ($kprot = 0.1) !proton shifts
!evaluate ($kprotd = 0.1) !proton shifts
evaluate ($krama = 0.002) !rama
evaluate ($kandb = 0.001)
evaluate ($kimdb = 0.001)
evaluate ($kramalr = 0.001) !long range rama
evaluate ($kvirt1doverall=0.0001)
evaluate ($kvirt1d=0.001)
evaluate ($kvirt2d=0.001)
evaluate ($kvirt3d=0.001)
evaluate ($knuc = 0.001) !rama
evaluate ($kdip = 1.0) !dipolar
!---------------------------------------------------------------------------
! Read experimental restraints
!set message off echo off end
set echo on message on end
noe
nres = 75000
class all
@../bla0.2.tbl
end
noe
ceiling 1000
averaging all sum
potential all square
scale all $knoe
sqconstant all 1.0
sqexponent all 2
end
!set message off echo off end
set message on echo on end
restraints dihed
reset
scale $kcdi
nass = 5000
@../bla.dih
@../talosgood.tbl
end
!set message on echo on end
evaluate ($ksani = 0.01)
evaluate ($ksani_CH = 1.0*$ksani)
evaluate ($ksani_CACO = 0.035*$ksani)
evaluate ($ksani_NCO = 0.050*$ksani)
evaluate ($ksani_HNC = 0.108*$ksani)
evaluate ($ksani_prot = 1.0*$ksani)
evaluate ($ksani_dna = 0.25*$ksani)
evaluate ($ksani_CH_dna = 1.0*$ksani)
sani
nres=1600
class JNH
force $ksani
potential harmonic
coeff 0.0 5.817 0.326
!@dip.xplor !dipolar coupling restraints
end
evaluate ($rcon = 0.003)
parameters
nbonds
atom
nbxmod 4
wmin = 0.01 ! warning off
cutnb = 4.5 ! nonbonded cutoff
tolerance 0.5
repel= 0.9 ! scale factor for vdW radii = 1 (
L-J radii)
rexp = 2 ! exponents in (r^irex -
R0^irex)^rexp
irex = 2
rcon=$rcon ! actually set the vdW weight
end
end
rama
nres=10000
!set message off echo off end
end
set message on echo on end
! Fixing the axis using harmonic restraint
! leave out, let both rotate
vector do (refx=x) (all)
vector do (refy=y) (all)
vector do (refz=z) (all)
constraints fix (resid 500 and name OO) end
evaluate ($cool_steps = 12000)
!evaluate ($cool_steps = 6000)
evaluate ($init_t = 3000.01)
vector do (mass = 100.0) (not resid 500 )
vector do (mass = 30.0) (resid 500 )
vector do (fbeta = 10.0) (all) ! coupling to
heat bath
coor copy end
{* Generate Structures 1 -> 10 *}
evaluate ($count =0)
while ($count < 100)
loop structure
evaluate ($count = $count + 1)
{====>} {*Filename(s) for
embedded coordinates.*}
vector do (x=xcomp) (all)
vector do (y=ycomp) (all)
vector do (z=zcomp) (all)
evaluate ($ini_prot = 0.5) evaluate ($fin_prot
= 7.5)
evaluate ($ini_protd = 0.1) evaluate
($fin_protd = 1.5)
evaluate ($ini_rad = 0.9) evaluate ($fin_rad
= 0.78)
evaluate ($ini_con= 0.004) evaluate ($fin_con=
4.0)
evaluate ($ini_ang = 0.4) evaluate ($fin_ang =
1.0)
evaluate ($ini_imp = 0.1) evaluate ($fin_imp =
1.0)
evaluate ($ini_noe = 2.0) evaluate ($fin_noe =
30.0)
evaluate ($knoe = $ini_noe) ! slope of NOE
potential
evaluate ($ini_rama = 0.002) evaluate
($fin_rama = 1.0)
evaluate ($krama = $ini_rama)
evaluate ($ini_lr = 0.0002) evaluate ($fin_lr =
0.15)
evaluate ($kramalr = $ini_lr)
evaluate ($ini_nuc = 1.000) evaluate ($fin_nuc
= 2.0)
evaluate ($knuc = $ini_nuc)
evaluate ($virt1d=$kramalr)
evaluate ($virt2d=$kramalr)
evaluate ($virt3d=$kramalr)
evaluate ($ini_andb = 0.001) evaluate
($fin_andb = 1000.0)
evaluate ($kandb = $ini_andb)
evaluate ($ini_imdb = 0.001) evaluate
($fin_imdb = 2000.0)
evaluate ($kimdb = $ini_imdb)
evaluate ($ini_kbb_a = 500.0) evaluate
($fin_kbb_a = 100.0)
evaluate ($kbbang = $ini_kbb_a)
evaluate ($ini_kbb_i = 500.0) evaluate
($fin_kbb_i = 10.0)
evaluate ($kbbimp = $ini_kbb_i)
evaluate ($kcdi = 10.0) ! torsion angles
!!evaluate ($ini_sani = 0.01) evaluate
($fin_sani = 1.0)
!!evaluate ($ksani = $ini_sani) !
!!evaluate ($ksani_CH = 1.0*$ksani)
!!evaluate ($ksani_CACO = 0.035*$ksani)
!!evaluate ($ksani_NCO = 0.050*$ksani)
!!evaluate ($ksani_HNC = 0.108*$ksani)
evaluate ($ksani_prot = 1.0*$ksani)
!!evaluate ($ksani_CH_dna = 1.0*$ksani)
!!sani class JNH force $ksani end
!!sani class JCACO force $ksani_CACO end
!!sani class JNCO force $ksani_NCO end
!!sani class JCH force $ksani_CH end
!!sani class JHNC force $ksani_HNC end
sani class JNH force $ksani end
!!sani class JCHd force $ksani_CH_dna end
{evaluate ($kprot = $ini_prot) !proton shifts
evaluate ($kprotd = $ini_protd) !proton shifts}
flags
exclude *
include bonds angl impr vdw noe cdih rama sani dihe
end
noe
averaging all sum
potential all square
scale all $knoe
sqconstant all 1.0
sqexponent all 2
end
restraints dihed
scale $kcdi
end
rama
end
evaluate ($rcon = 1.0)
parameters
nbonds
atom
nbxmod 4
wmin = 0.01 ! warning off
cutnb = 100 ! nonbonded cutoff
tolerance 45
repel= 1.2 ! scale factor for vdW radii = 1 (
L-J radii)
rexp = 2 ! exponents in (r^irex -
R0^irex)^rexp
irex = 2
rcon=$rcon ! actually set the vdW weight
end
end
constraints
interaction (not name ca) (all)
weights * 1 angl 0.4 impr 0.1 vdw 0 elec 0 end
interaction (name ca) (name ca)
weights * 1 angl 0.4 impr 0.1 vdw 1.0 end
end
dynamics verlet
nstep=5000 !
timestep=0.005 !
iasvel=maxwell firsttemp= $init_t
tcoupling = true
tbath = $init_t
nprint=50
iprfrq=0
ntrfr = 99999999
end
parameters
nbonds
atom
nbxmod 4
wmin = 0.01 ! warning off
cutnb = 4.5 ! nonbonded cutoff
tolerance 0.5
repel= 0.9 ! scale factor for vdW radii = 1 (
L-J radii)
rexp = 2 ! exponents in (r^irex -
R0^irex)^rexp
irex = 2
rcon =1.0 ! actually set the vdW weight
end
end
evaluate ($kcdi = 200)
restraints dihed
scale $kcdi
end
evaluate ($final_t = 100) { K }
evaluate ($tempstep = 25) { K }
evaluate ($ncycle = ($init_t-$final_t)/$tempstep)
evaluate ($nstep = int($cool_steps*4.0/$ncycle))
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/$ncycle))
evaluate ($k_ang = $ini_ang)
evaluate ($ang_fac = ($fin_ang/$ini_ang)^(1/$ncycle))
evaluate ($k_imp = $ini_imp)
evaluate ($imp_fac = ($fin_imp/$ini_imp)^(1/$ncycle))
evaluate ($noe_fac = ($fin_noe/$ini_noe)^(1/$ncycle))
evaluate ($knoe = $ini_noe)
evaluate ($rama_fac =
($fin_rama/$ini_rama)^(1/$ncycle))
evaluate ($krama = $ini_rama)
evaluate ($lr_fac = ($fin_lr/$ini_lr)^(1/$ncycle))
evaluate ($kramalr = $ini_lr)
evaluate ($nuc_fac = ($fin_nuc/$ini_nuc)^(1/$ncycle))
evaluate ($knuc = $ini_nuc)
evaluate ($virt1d=$kramalr)
evaluate ($virt2d=$kramalr)
evaluate ($virt3d=$kramalr)
evaluate ($andb_fac =
($fin_andb/$ini_andb)^(1/$ncycle))
evaluate ($kandb = $ini_andb)
evaluate ($imdb_fac =
($fin_imdb/$ini_imdb)^(1/$ncycle))
evaluate ($kimdb = $ini_imdb)
evaluate ($kbb_fac_i =
($fin_kbb_i/$ini_kbb_i)^(1/$ncycle))
evaluate ($kbb_fac_a =
($fin_kbb_a/$ini_kbb_a)^(1/$ncycle))
evaluate ($kbbang = $ini_kbb_a)
evaluate ($kbbimp = $ini_kbb_i)
!!evaluate ($sani_fac =
($fin_sani/$ini_sani)^(1/$ncycle))
!!evaluate ($ksani = $ini_sani)
!!evaluate ($ksani_CH = 1.0*$ksani)
!!evaluate ($ksani_CACO = 0.035*$ksani)
!!evaluate ($ksani_NCO = 0.050*$ksani)
!!evaluate ($ksani_HNC = 0.108*$ksani)
!!evaluate ($ksani_prot = 1.00*$ksani)
!!evaluate ($ksani_CH_dna = 1.00*$ksani)
flags
exclude *
include bonds angl impr vdw noe rama cdih sani dihe
end
vector do (vx = maxwell($bath)) (all)
vector do (vy = maxwell($bath)) (all)
vector do (vz = maxwell($bath)) (all)
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*$radfact))
evaluate ($k_ang = $k_ang*$ang_fac)
evaluate ($k_imp = $k_imp*$imp_fac)
evaluate ($knoe = $knoe*$noe_fac)
evaluate ($krama = $krama*$rama_fac)
evaluate ($kramalr = $kramalr*$lr_fac)
evaluate ($knuc = $knuc*$nuc_fac)
evaluate ($virt1d=$kramalr)
evaluate ($virt2d=$kramalr)
evaluate ($virt3d=$kramalr)
evaluate ($kandb = $kandb*$andb_fac)
evaluate ($kimdb = $kimdb*$imdb_fac)
evaluate ($kbbang = $kbbang*$kbb_fac_a)
evaluate ($kbbimp = $kbbimp*$kbb_fac_i)
!!evaluate ($ksani = $ksani*$sani_fac)
!!evaluate ($ksani_CH = 1.0*$ksani)
!!evaluate ($ksani_CACO = 0.035*$ksani)
!!evaluate ($ksani_NCO = 0.050*$ksani)
!!evaluate ($ksani_HNC = 0.108*$ksani)
!!evaluate ($ksani_prot = 1.00*$ksani)
!!evaluate ($ksani_dna = 0.25*$ksani)
!!evaluate ($ksani_CH_dna = 1.00*$ksani)
constraints interaction (all) (all) weights
* 1 angles $k_ang improper $k_imp
end end
parameter
nbonds
cutnb=4.5 rcon=$k_vdw nbxmod=4 repel=$radius
end end
noe scale all $knoe end
!! sani class JNH force $ksani end
!! sani class JCACO force $ksani_CACO end
!! sani class JNCO force $ksani_NCO end
!! sani class JCH force $ksani_CH end
!! sani class JHNC force $ksani_HNC end
!! sani class JNH force $ksani end
!!rama
!!end
dynamics verlet
nstep=$nstep timestep=0.005 iasvel=current
firsttemp= $bath
tcoupling = true tbath = $bath
nprint=$nstep iprfrq=0
ntrfr = 99999999
end
end loop cool
mini powell nstep= 250 nprint= 50 end
! remove bumps
constraints
interaction (all) (all)
weights vdw 5 end
end
mini powell nstep= 250 nprint= 50 end
print threshold=0.5 noe
evaluate ($rms_noe=$result)
evaluate ($violations_noe=$violations)
print threshold=10. cdih
evaluate ($rms_cdih=$result)
evaluate ($violations_cdih=$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,cidh,vdw, noe
remarks energies: $ener, $bond, $angl, $impr,
$cdih, $vdw, $noe
remarks
===============================================================
remarks bonds,angles,impropers,cdih,noe
remarks
$rms_bonds,$rms_angles,$rms_impropers,$rms_cdih,$rms_noe
remarks
===============================================================
remarks cdih end_coup end_coup_gly
noe
remarks violations : $violations_cdih
$violations_noe
remarks
===============================================================
{====>} {*Name(s) of the family
of final structures.*}
evaluate ($file = "sa_xplor_" + encode($count) +
".pdb")
write coor output= $file end
end loop structure
stop
Best regards
Angelo Figueiredo
Phd student (University of East Anglia -Norwich, UK)
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