Dear Bozidar,

Thank you for help. Your hint(to put '' instead of '0') looks to work so far. Regarding the fact that coordinates for the loop were zeroed, I did this in order to get a de novo loop prediction.

Adrian

Quoting Bozidar Jerkovic bozidar@oboe.rockefeller.edu:

> > Dear Adrian, > > A simple answer to your question is: you specified a non-existing > segment of the protein for the loop optimization: > SELECTION_SEGMENT = '151:0' '154:0', SELECTION_STATUS = 'initialize' > > In your pdb file there is no '0' chain: > ATOM 1165 CD2 LEU 150 44.348 42.655 43.046 1.00 15.23 C > ATOM 1166 N GLY 151 0.000 0.000 0.000 1.00 16.38 N > ATOM 1167 CA GLY 15 0.000 0.000 0.000 1.00 15.57 C > > This results in MODELLER selecting the whole protein to perform 'loop' > routine on it: > Number of all, selected real atoms : 1480 1480 > > Another thing I noticed is that you have compresses all the residues you > are selecting into one point? Is there any specific reason for this? > ATOM 1166 N GLY 151 0.000 0.000 0.000 1.00 16.38 N > ATOM 1167 CA GLY 151 0.000 0.000 0.000 1.00 15.57 C > ATOM 1168 C GLY 151 0.000 0.000 0.000 1.00 16.31 C > > MODELLER complains about this though, but it keeps on: > serious non-bonded atom clash: 1143 1148 0.000 > serious non-bonded atom clash: 1143 1149 0.000 > serious non-bonded atom clash: 1143 1150 0.000 > > Energies are way off the charts: > Initial value of energy before optimization : 477452.2400 > Current energy : 476905.9000 > Maximal energy, step : 525495.1200 > 28 > Minimal energy, step : 449273.2100 > 81 > Average energy, stand.dev. : 506870.8100 > 15563.8500 > > What causes MODELLER to become a memory hog is the fact that you > unintentionally tried to perform an ab initio calculation of the whole > protein. I myself almost crashed our main Linux machine in the group, > running your top file. A job used up 92% of the available memory at one > point. > > After I corrected the .top file: > SELECTION_SEGMENT = '151:' '154:', SELECTION_STATUS = 'initialize' > > Energy returned to normal: > Initial value of energy before optimization : 27.4512 > Current energy : 4.5270 > Maximal energy, step : 67.8339 > 34 > Minimal energy, step : 25.2391 > 363 > Average energy, stand.dev. : 43.2928 > 10.7857 > > ... and MODELLER produced a beautiful model ;-) > > Summa sumarum: > One has to make sure that when s/he selects a segment of the protein, > using 'res_ID:chain_ID' convention (which is updated for the 6v2 > release), that there is an existing chain_ID there. This is actually > quite a common mistake many users do: their pdb has a chain_ID, and they > omit it in their top file (just opposite of what you did). > > I am still curious why you have compressed all the loop residues into a > single point (why those residues have all the coordinates equal to > zero)? It worked, because those resides were brought back into the > protein in the model MODELLER calculated, which is obviously good, and > their energy is also fine. If this is some empirical finding, and not > missing coordinates, I would certainly like to learn more about it. > > ...and there is no memory leak, thankfully ;-) > > All the best and happy modeling, > Bozidar > > > > -----Original Message----- > From: AA_Canutescu@fccc.edu [mailto:AA_Canutescu@fccc.edu] > Sent: Wednesday, April 17, 2002 6:49 PM > To: Bozidar Jerkovic > Subject: Re: MODELLER > > > Dear Bozidar, > > > > > Yes I am aware of this one. I think it may have to do with static vs. > > dynamic linking. > > It's not obvious to me why could be a linking problem, but anyway it's > interesting this happens only for certain input files. For the input > data sets that generate this bug, the bug is repro(reproducible -all the > time). There is no situation(as far as I tested) in which for the same > input data to get the software working sometime and not working other > time. It just doesn't work -all the time - for that input data. > > > > What did you mean by "repro"? > > An error that is exactly reproducible under any circumstances. It's used > in programers' jargon. > > > The other problem, that is actually the most serious one is also repro. > For certain input data sets, modeller starts allocating huge amounts of > memory (about 1GB/min on my machine). This indicates a serious memory > leak. I got my kernal crashed twice today because of this, so I have to > wait for your patch before using again modeller. > > I will attach again an input data set that leads to this memory leak. > > Everything is run on RedHat 7.2 on x86 architecture. > > Thanks, > Adrian > > > > > > Thanks for these reports. It's sometimes hard for us to catch > > everything. > > > > Best, > > Bozidar > > > > > > On 17/4/02 5:33 PM, "AA_Canutescu@fccc.edu" AA_Canutescu@fccc.edu > > wrote: > > > > > Dear Bozidar, > > > > > > I have another problem to report, besides the memory leak one. For > > some > > > reasons, I got in certain situations the following error: > > > > > > ? FORTRAN Runtime Error: > > > ? Illegal character in numeric input > > > ? READ(UNIT=INTERNAL,... > > > > > > I wasn't able to track down any cause, and the error message is not > > very > > > explanatory to me. I would appreciate if you could give me a hint > > about this > > > sitation. This situation is a repro one, like also the memory leak > > one. I run > > > everything > > > > > > > > > > > > Thank you, > > > > > > Adrian > > > > > > > > > Quoting Bozidar Jerkovic bozidar@salilab.org: > > > > > >> > > >> Hi, > > >> > > >> Loop is definitely supported ;-). I'll see what's going on. > > >> > > >> Best, > > >> Bozidar > > >> > > >> > > >> On 10/4/02 1:18 PM, "AA_Canutescu@fccc.edu" AA_Canutescu@fccc.edu > > >> wrote: > > >> > > >>> 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 > > >>>> > > >>>> > > >>> > > >> > > >> > > > > > > > > >