Re: [modeller_usage] Restraints Problem

["akshay17" <>]

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
> > --
> > 
> > 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 : , 
> 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 : ,  
Web   : www.olemiss.edu

Attachment: angim_06.log
Description: Binary data

Attachment: Constraints_USER.rsr
Description: Binary data

Attachment: angim_06.top
Description: Binary data