Dear Sir
I tried rearranging parameters and Atom_ids which were written in wrong order in my .rsr file. This time, it says "segmentation fault (core dumped)". I recognize my problem somewhat similar to Mr. Daniele Bemporad's but as advised by you, i think in his .rsr file also, the parameters and Atom_ids are other way around. Anyway, i guess there might be some other problem apart from that. I am attaching my .rsr, .top & .log files.
Is it possible that the User restraints i am giving might be unreasonable to be met during the model generation due to which it halts? I am not sure.
Thanks for your help. Akshay Patny > > > On Tue, Jul 20, 2004 at 12:05:36AM -0500, akshay17 > > > wrote: Dear Sir, I tried removing Extra lines from my > > > .rsr file and still got the following error. > > > > > > > > > __________________________________________________________ > > > __ _ Executing Modeler Additional output in file > > > angim_06.log and in angim_06.log.moltabfile, > > > angim_06.log.restabfile, angim_06.log.viotabfile* > > > > > > lib-4190 : UNRECOVERABLE library error > > > A numeric input field contains an invalid character. > > > > > > Encountered during a list-directed READ from an > > > internal file (character variable) > > > IOT Trap > > > Abort (core dumped) > > > > > > > > > __________________________________________________________ > > __ _ > > > > Please advise. Shall, i write MODELLER 5 or MODELLER > > > 6v2 in my .rsr file. I am attaching my .rsr file > again. > > > The format of your restraints file is incorrect; see > > http://salilab.org/modeller/manual/node98.html. The > > first line must read either 'MODELLER5 VERSION: MODELLER > > FORMAT' or 'MODELLER5 VERSION: USER FORMAT'. There is no > > 'MODELLER6v2' format. Additionally, your user format > > lines are incorrect - the format should be: > > > > Id Form Modality Feature Group Numb_atoms > > Numb_parameters 0 Parameters Atom_ids > > > > - i.e., you have your parameters and Atom_ids the wrong > > way round. Your restraints file should look something > > like the following: > > > > MODELLER5 VERSION: USER FORMAT > > R 2 1 1 22 2 2 0 5.0 1.0 NZ:102 > > OD1:278 R 2 1 1 22 2 2 0 5.0 1.0 NZ:102 > > CZ:92 R 2 1 1 22 2 2 0 5.0 1.0 CZ:167 > > CG:263 R 2 1 1 22 2 2 0 5.0 1.0 NZ:199 > > CZ:259 R 2 1 1 22 2 2 0 5.0 1.0 OH:292 > > OD1:295 R 2 1 1 22 2 2 0 5.0 1.0 OH:292 > > OD1:111 R 2 1 1 22 2 2 0 5.0 1.0 NZ:240 > OD1:237 > > > Ben Webb, Modeller Caretaker > > -- > > modeller-care@salilab.org > > http://www.salilab.org/modeller/ Modeller mailing list: > > http://salilab.org/mailman/listinfo/modeller_usage > > > > Akshay Patny > (Graduate Student @ PhD) > Department of Medicinal Chemistry > School of Pharmacy, University of Mississippi > 417, Faser Hall, University, MS - 38677 > Tel : 662-915-1286(Off.), 662-236-3059(Res.) > E-mail : akshaypatny@indiatimes.com, akshay17@olemiss.edu > Web : www.olemiss.edu > >
Akshay Patny (Graduate Student @ PhD) Department of Medicinal Chemistry School of Pharmacy, University of Mississippi 417, Faser Hall, University, MS - 38677 Tel : 662-915-1286(Off.), 662-236-3059(Res.) E-mail : akshaypatny@indiatimes.com, akshay17@olemiss.edu Web : www.olemiss.edu
On Wed, Jul 21, 2004 at 11:34:39AM -0500, akshay17 wrote: > I tried rearranging parameters and Atom_ids which were > written in wrong order in my .rsr file. This time, it > says "segmentation fault (core dumped)". I recognize my > problem somewhat similar to Mr. Daniele Bemporad's but as > advised by you, i think in his .rsr file also, the > parameters and Atom_ids are other way around. Anyway, i > guess there might be some other problem apart from that. I > am attaching my .rsr, .top & .log files. > > Is it possible that the User restraints i am giving might be > unreasonable to be met during the model generation due to > which it halts? I am not sure.
I cannot diagnose your problem without all of the necessary inputs; you seem to have forgotten to send angim_06.pir and P_1L9H.pdb. Send them directly to me at modeller-care@salilab.org, and I'll take a look.
Ben Webb, Modeller Caretaker
On Wed, Jul 21, 2004 at 11:34:39AM -0500, akshay17 wrote: > I tried rearranging parameters and Atom_ids which were > written in wrong order in my .rsr file. This time, it > says "segmentation fault (core dumped)". I recognize my > problem somewhat similar to Mr. Daniele Bemporad's but as > advised by you, i think in his .rsr file also, the > parameters and Atom_ids are other way around. Anyway, i > guess there might be some other problem apart from that. I > am attaching my .rsr, .top & .log files.
With all the provided input files, I have been able to run your same calculation here. It runs to completion with no errors with mod6v2. Therefore it would appear to be a bug in the version of Modeller distributed with Insight II. We do not build or support Insight II; you will have to take up this problem with Accelrys. Alternatively, you can run your input files through the academic mod6v2, assuming you qualify for an academic license (your email address would suggest that you do).
Ben Webb, Modeller Caretaker
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