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: AA_Canutescu@fccc.edu [mailto:AA_Canutescu@fccc.edu] > 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 bozidar@salilab.org: > > > > > 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, "AA_Canutescu@fccc.edu" AA_Canutescu@fccc.edu > > 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