[xplor-NIH] Re: Can you check the protocol?
John Kuszewski
John.Kuszewski at cbel.cit.nih.gov
Thu Jul 18 19:29:39 EDT 2002
Hi Ishima-san,
I've attached a slightly modified version of your file to this email.
I just changed the high temperature from 2000K to 3000K and the
number of cooling steps from 3000 to 12000. It should work better,
but let me know if it doesn't.
--JK
Rieko Ishima wrote:
>
> Hi John
>
> I ran xplor using the protocol (with dipolar coupling) that you and Kirstin
> worked for me.
> Although the old dgsa protocol minimizes structures very well, the protocol
> with dipolar coupling did not. I mean that b-sheets in rigid part are not
> superimposed well (but folding is O.K.). I ran it without sani part, but
> the results were almost the same.
>
> The data I used are noe, dihedral couplings (not so much), and N-Hn dipolar
> couplings. Can you check again that the protocol is supposed to be enough
> to minimize the structure even in such a data set?
>
> Thank you for your help.
>
> Rieko
>
> ------------------------------------------------------------------------
>
> sa_dipo4.inpName: sa_dipo4.inp
> Type: Plain Text (text/plain)
>
> ------------------------------------------------------------------------
> ---------------------------<>--------------------------------
> Rieko Ishima, Ph.D.
>
> Bldg 30, Rm 109, NIH, NIDCR,
> 30 Convent Dr., Bethesda, MD 20892-4307, USA
> e-mail: rishima at dir.nidcr.nih.gov
> tel: 301-402-3160 (or 301-402-3149)
> fax: 301-402-5321 (or 301-480-0240)
--
Dr John Kuszewski
301-594-5831 (voice)
301-402-2867 (fax)
John.Kuszewski at nih.gov-------------- next part --------------
REMARKS This protocol allows computer to select dimer noes
REMARKS very slow cooling with increase of vdw
evaluate ($seed=65748309)
set seed $seed end
!----------------------------------------------------------------------
! read in the PSF file and initial structure
! read in the PSF file and initial structure
structure @all.psf @axis_500.psf end
parameter
{====>}
! @TOPPAR:parallhdg_procheck.pro ! the one with proline in seq.
@TOPPARN:parallhdg_pc_new.pro
@TOPPAR:parnah1er1_mod_new.inp
@TOPPAR:par_axis_3.pro
bond CP NH3 $kbon 1.473 ! CP - proline at N terminus
angle CP CP NH3 $kang 103.2 ! CP - proline at N terminus
angle HA CP NH3 $kang 109.5 ! CP - proline at N terminus
angle CT NH3 CP $kang 112.0 ! CP - proline at N terminus
improper HC HC CT CP 50.0 0 -70.0 ! N-term Pro
improper HA HA CP NH3 $kchi 0 -70.874 ! CP methylene
end
coor @all.pdb !protein pdb + axis pdb
!delete select (resid 1:2) end
!delete select (resid 48:53) end
!delete select (resid 85:95) end
! set the weights for the experimental energy terms
evaluate ($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
noe
nres = 16000
class all
@hchcnoe.xplor
@noesy15n.xplor
@hbond.xplor
end
! set echo on message on 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 $kcdi
nass = 5000
@angle.xplor
end
!set message on echo on end
evaluate ($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=$rcon ! actually set the vdW weight
end
end
rama
nres=10000
!set message off echo off end
@/net/occam3/jaison/xplor-nih-1.0.6-bin/databases/torsion_gaussians/shortrange_g
aussians.tbl
@/net/occam3/jaison/xplor-nih-1.0.6-bin/databases/torsion_gaussians/new_shortran
ge_force.tbl
@/net/occam3/jaison/xplor-nih-1.0.6-bin/databases/torsion_gaussians/all_na_gauss
ians.tbl
@/net/occam3/jaison/xplor-nih-1.0.6-bin/databases/torsion_gaussians/force_nuclei
c.tbl
end
set message on echo on end
@/net/occam3/jaison/xplor-nih-1.0.6-bin/databases/torsion_gaussians/newshortrang
e_setup.tbl
@/net/occam3/jaison/xplor-nih-1.0.6-bin/databases/torsion_gaussians/setup_nuclei
c_new.tbl
! Fixing the axis using harmonic restraint
! leave out, let both rotate
vector do (refx=x) (all)
vector do (refy=y) (all)
vector do (refz=z) (all)
constraints fix (resid 500 and name OO) end
evaluate ($cool_steps = 12000)
evaluate ($init_t = 3000.01)
vector do (mass = 100.0) (not resid 500 )
vector do (mass = 30.0) (resid 500 )
vector do (fbeta = 10.0) (all) ! coupling to heat bath
coor copy end
{* Generate Structures 1 -> 10 *}
evaluate ($count =0)
while ($count < 5)
loop structure
evaluate ($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
end
noe
averaging all sum
potential all square
scale all $knoe
sqconstant all 1.0
sqexponent all 2
end
restraints dihed
scale $kcdi
end
rama
@/net/occam3/jaison/xplor-nih-1.0.6-bin/databases/torsion_gaussians/new_shortran
ge_force.tbl
!@/net/octave2/clore/xplor_40/gaussians/longrange_4D_hstgp_force.tbl
!@/net/octave2/clore/xplor_40/gaussians/virtualTA_force_hstgp.tbl
@/net/occam3/jaison/xplor-nih-1.0.6-bin/databases/torsion_gaussians/force_nuclei
c.tbl
end
evaluate ($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*$ksani)
flags
exclude *
include bonds angl impr vdw noe rama cdih sani
end
vector do (vx = maxwell($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 $ksani end
rama
@/net/occam3/jaison/xplor-nih-1.0.6-bin/databases/torsion_gaussians/new_shortran
ge_force.tbl
!@/net/octave2/clore/xplor_40/gaussians/longrange_4D_hstgp_force.tbl
!@/net/octave2/clore/xplor_40/gaussians/virtualTA_force_hstgp.tbl
@/net/occam3/jaison/xplor-nih-1.0.6-bin/databases/torsion_gaussians/force_nuclei
c.tbl
end
dynamics verlet
nstep=$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
print threshold=0.5 noe
evaluate ($rms_noe=$result)
evaluate ($violations_noe=$violations)
print threshold=5. 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)
sani print threshold=0.5 class JNH end
evaluate ($rms_sani_JNH=$result)
evaluate ($viol_sani_JNH=$violations)
remarks ===============================================================
remarks overall,bonds,angles,improper,cidh,vdw, noe, rama, sani
remarks energies: $ener, $bond, $angl, $impr, $cdih, $vdw, $noe, $rama,
$sani
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 $end_viols $end_viols_g
$violations_noe
remarks shifts: $viol_shift
remarks ===============================================================
remarks ==================
remarks sani NH
remarks RMS sani: $rms_sani_JNH
remarks R-factor sani: $R_JNH
remarks viol sani: $viol_sani_JNH
remarks ===============================================================
{====>} {*Name(s) of the family of final structures.*}
evaluate ($file = "sa_dip4_" + encode($count) + ".sa")
write coor output= $file end
end loop structure
stop
More information about the Xplor-nih
mailing list