Dear Charles:
Thank you very much for your response. (John Kuszewski also responded.)
I've now encountered the same problem with a single (non-nested) "while"
loop. The legacy script (attached), and a command file that calls the
script (attached), work fine using XPLOR 98.1 under UNIX (two minimized
structures are produced), but with XPLOR-NIH under Linux, the first
structure is produced, and then the while loop error occurs:
%X-PLOR-ERR: unrecognized command:
while
^^^^
Also, is ABNR minimization supported by XPLOR-NIH? (The line "mini abnr
nstep=2000 end" was not recognized). Are there alternatives to Powell? I
often encounter situations where ABNR works but Powell fails.
Thanks again for all of your help!
Keith
[EMAIL PROTECTED] wrote:
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Hello Keith--
I am (finally) moving from X-PLOR to XPLOR-NIH, and I've ecountered a
problem with legacy scripts containing nested while loops. The nesting
worked in XPLOR 98.1 under UNIX, but gives errors when the exact same
script is run in XPLOR-NIH 2.15.0 under Linux.
It would be quite helpful if you could send a very short example script
which exhibits the problem.
Nested while loops are used extensively in legacy XPLOR scripts, and
they should work fine. Do note that Xplor-NIH maintains compatibilty
with X-PLOR 3.851 and it's conceivable that there are slight differences
with XPLOR 98.1, but should be easily worked around.
best regards--
Charles
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{ ************************************************************************** }
{ A straight minimization procedure for a familu of structures. }
{ }
{ ************************************************************************** }
parameter
! {===>} @../top/parall_kc.pro
{===>} @../top/parall_kc_fixarg.pro
@$ligparfile
nbfix S S 462 13.6 462 13.6
end
set echo=off end
set message=off end
{===>} structure @$psffile1 @$psffile2 end { read
structure files }
evaluate ($currenti = $firsti )
{ ************************************************************************** }
{ Construct pdb file names. Read in coordinates. }
{ ************************************************************************** }
while ($lasti GE $currenti) loop main
evaluate ( $pdb1 = $pdbfilein + encode($currenti) + ".pdb" )
coordinates @@$pdb1 { read the coordinates }
{ ************************************************************************** }
{ Read in noe constraints and set up energy functions. }
{ ************************************************************************** }
evaluate ($knoe = 50.0) { set constants for the experimental energy }
flags
include noe cdih elec
exclude dihe
end
noe { read NOE restraints }
reset
nrestraints = 8000 { allocate space for NOEs }
ceiling = 100 { maximum force constant that is allowed }
class all @@$noefile { NOE restraint file }
@@$disulfides { disulfide bond distance restraints }
averaging all sum
potential all square
scale all $knoe
sqconstant all 1.0
sqexponent all 2
end
{ ************************************************************************** }
{ Read in torsion constraints and set up energy functions. }
{ ************************************************************************** }
restraints dihedral { next 4 lines should eliminate NASS error }
reset
nassign = 2000
end
@@$anglefile { read NMR torsion angle restraints }
{===>} @@$fixfile
parameters { setup the repulsive energy term }
nbonds
cutnb = 8.5 {changed from 8.0}
ctofnb = 7.5
ctonnb = 6.5
rdiel
eps = 4.0 {changed from 2.0}
switch vswitch
nbxmod = 5
tolerance 0.3
repel = 0.0
rexp = 2 { exponents in (r^irex - R0^irex)^rexp }
irex = 2
rcon = 4 { actually set the vdW weight }
end
end
{ ************************************************************************** }
{ Stage 1: The initial minimization ensures the geometry of the initial }
{ structure is good. }
{ ************************************************************************** }
{ mini abnr nstep=2000 end }
mini powell nstep=2000 drop = 10.0 end
{ ************************************************************************** }
{ Write out final coordinates. Get next file. }
{ ************************************************************************** }
evaluate ( $pdb2 = $pdbfileout + encode($currenti) + ".pdb" )
write coordinates output=$pdb2 end { write coordinates }
evaluate ( $currenti=$currenti+1 )
end loop main
stop
evaluate ( $psffile1 = "a.psf" )
evaluate ( $psffile2 = "b.xpsf" )
evaluate ( $ligparfile = "b.xprm")
evaluate ( $pdbfilein = "c_" )
evaluate ( $pdbfileout = "d_" )
evaluate ( $firsti = 1 )
evaluate ( $lasti = 2 )
evaluate ( $noefile = "noe.tbl")
evaluate ( $disulfides = "null.file")
evaluate ( $anglefile = "dih.tbl")
evaluate ( $fixfile = "fixnone.tbl")
evaluate ( $numstep = 2000)
@../input/minelec_sum_prot_lig.inp
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