Re: [modeller_usage] Restraints Problem
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.
Thanks Akshay Patny.
> On Fri, Jul 16, 2004 at 04:41:03PM -0500, akshay17 wrote: > > I recently joined Modeller mailing list and i am also > > new to the program. > > > > I am using Modeler as an interface from Insight II. I > > have been trying to give my own restraints during the > > model generation as a .rsr file. I tried using both the > > MODELER FORMAT as well as the USER FORMAT restraint > > files. The problem is whenever i submit my job, it does > > not complete and gives error in log file one of which is > > the following: "Incorrect record identifier in restraint > file; card:" > > You have blank lines in your restraints file; Modeller6v2 > doesn't understand these. Take them out and all should be > well. > > 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
[Attachment: Constraints_USER.rsr]
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 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
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akshay17 -
Modeller Caretaker