Hi,
Everything is fine, but the format has changed a little bit, instead of
'refine2' use 'refine_2'
in your LOOP_MD_level call (refine_1, refine_2, refine_3)
Andras
Bozidar Jerkovic wrote:
>
> Thanks,
> Bozidar
>
> -----Original Message-----
> From: [">mailto:]
> Sent: Wednesday, April 10, 2002 1:18 PM
> To: Bozidar Jerkovic
> Subject: Re: MODELLER
>
> Hi,
>
> I attached a tar.gz that contains top, log and pdb input file. In
> case 'loop' routine is not anymore supported in mod6v1, what would be
> a get around for my problem?
>
> Thanks for your help.
>
> Adrian
>
> Quoting Bozidar Jerkovic <>:
>
> >
> > Hi,
> >
> > Can you please send me your .top and .log and all input files and
> > I'll
>
> > run it here. I can't actually see which part of .top fails. I
> > presume it's "CALL
> > ROUTINE = 'loop' # do loop modeling", but I don't wanna guess.
> >
> > Best,
> > Bozidar
> >
> >
> >
> > On 8/4/02 3:24 PM, "" <>
> > wrote:
> >
> > > Dear Bozidar,
> > >
> > >
> > > I downloaded the last version of MODELLER and I am running into
> > > some problems. For the time being, I use MODELLER mostly for loop
> > > modeling.
> > Using
> > > the
> > > previous version(mod6a), I used to create a top file like this,
> > > and
> > everything
> > > worked ok:
> > >
> > > INCLUDE
> > > SET OUTPUT_CONTROL = 1 0 0 1 0 # Set to 1 1 1 1 0 for
> debugging.
> > > SET SEQUENCE = '1dysA_47-50'
> > > SET LOOP_MODEL = '1dysA_47-50.pdb'
> > > SET LOOP_MD_LEVEL = 'refine2' # refine3 - fastest
> > > # refine2 - medium
> > > # refine1 - most thorough SET
> > > LOOP_STARTING_MODEL = 1 SET LOOP_ENDING_MODEL = 3 # number of
> > > loop models
> > > SET RAND_SEED = -38901 # change for different starting models
> > > CALL ROUTINE = 'loop' # do loop modeling
> > >
> > > # Pick model residues that need to be refined.
> > >
> > > SUBROUTINE ROUTINE = 'select_loop_atoms' # Uncomment if you also
> > > want
> > to
> > > optimize the environment:
> > > # SET SELECTION_SEARCH = 'SPHERE_SEGMENT', SPHERE_RADIUS = 6
> > > PICK_ATOMS SELECTION_SEGMENT = '47:A' '50:A', SELECTION_STATUS =
> > 'initialize'
> > > RETURN
> > > END_SUBROUTINE
> > >
> > >
> > > With the newest version of MODELLER that I downloaded last week,
> > doesn't work
> > > anymore. I receive an error message in the end of.log file like
> > > this:
> > >
> > > act10___551E> No such routine:
> > > recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
> > >
> > > Dynamically allocated memory at finish [B,kB,MB]:
> > 28478873
> > > 27811.400 27.160
> > > Starting time :
> 2002/04/08
> > > 14:20:40.274
> > > Closing time :
> 2002/04/08
> > > 14:20:51.421
> > > Total CPU time [seconds] :
> 11.00
> > >
> > >
> > > Could you help me please regarding this matter? Could you also
> > > tell me
> > if
> > > there is any dependency needed(some libraries, fortran, etc)? I am
> > using
> > > RedHat
> > > 7.2 with kernal 2.4.7-10
> > >
> > >
> > >
> > > Thanks,
> > >
> > > Adrian Canutescu
> >
> >
>
>
------------------------------------------------------------------------
> Name: mod_files.tar.gz
> mod_files.tar.gz Type: Unix Tape Archive (application/x-tar)
> Encoding: base64
--
,
Andras Fiser, PhD # phone: (212) 327 7216
The Rockefeller University # fax: (212) 327 7540
Box 270, 1230 York Avenue # e-mail:
New York, NY 10021-6399, USA # http://salilab.org/~andras