Dear Modellers,
What is the exact meaning of the columns in .rsr file? I think I have a pretty good idea for all of them except two, but wouldn't mind if someone can explain.
Happy modelling,
Mensur Dlakic
|>Hi, |> |>In principle, what you are trying to do is a fine idea and should be possible |>to do something along those lines with MODELLER. Your problem may be a bug in |>MODELLER or it may be a problem with the restraint file format as you use |it, or |>something else. There is no "1000" limitation on the number of |restraints. Are |>you specifying atoms by their integer indices or by their atom names (one has |>to use the corresponding restraint file format)? Are you using hydrogens, |>in which case the TOPOLOGY_MODEL has to be set to 1 and the GENERATE_TOPOLOGY |>command has to be executed with the top.lib topology library, which contains |>all hydrogens, not the default top_heav.lib? Are you defining pseudo atoms |>and using restraints on pseudo atoms (indicated by the second error message), |>the code for which is buggy? |> |>If this does not help, please email me the input files. |> |>Let's resolve this. |> |>Best, Andrej |> |> |>> Dear Modellers, |>> |>> I am using experimental NOE restraints to improve models in case of weak |>> homology between a target and its template. The NOE restraint file was |>> included as: |>> |>> READ_RESTRAINTS FILE = 'nmr_2igh.rsr' |>> |>> However, when the file contains many entries (>1000 restraints), the |>> following error message occurs: |>> |>> iup2crm_E> IUPAC atom not found in topology library: H |>> act34___E> indpsd(i) out of range; ireal, natm: 0 2953 |>> |>> The MODELLER runs fine when number of NOE entries is smaller than 500, |>> and the output model shows improvement when using NOE restraints. I |>> assume for restraint file with "MODELLER12 VERSION: USER FORMAT" has an |>> upper bound for number of allowed entries. Is there any way that I can |>> get around this problem? |>> |>> Thanks, |>> |>> -Dong Xu |>> http://compbio.ornl.gov/~nxy |>> |>> |> |> |>-- |>-- |>Andrej Sali, Assistant Professor |>The Rockefeller University, 1230 York Avenue, New York, NY 10021-6399 |>tel +1 212 327 7550; lab +1 212 327 7206 ; fax +1 212 327 7540 |>e-mail sali@rockefeller.edu; http://salilab.org
======================================================================== | Mensur Dlakic, PhD | Tel: (734) 764-3554 | | Howard Hughes Med Inst | Fax: (734) 763-9323 | | 4570 MSRB II | http://www-personal.umich.edu/~mensur/ | | 1150 W Medical Center Dr | | | Ann Arbor, MI 48109-0650 | E-mail: mensur@umich.edu | ========================================================================