[RNABuilder-help] Re: MMB issues

[Samuel Flores]

On Mar 25, 2014, at 12:06 PM, Erik Marklund <erik.marklund at chem.ox.ac.uk> wrote:

> Hi Sam,
> 
> How are things with you? Do I remember correctly that you've entered parenthood nowadays?

Yes!

> 
> I indended to use MMB for filling in a gap in a loop, just a single amino acid. Sounds trivial, but I can't get it to work. The protein looks like someone set of a bomb in the middle of it already at frame 1. Could you spot any obvious error in this input file below? The protein is a homodimer with a single amino acid missing at position 49.

The problem is that you are instantiating the chains directly using the “protein” command.  This automatically assigns sequential residue numbers based on the provided sequence, starting in this case with “2”. You should instead read the sequences from the PDB — this will conserve the residue numbering in the PDB file, including all gaps and insertions. Then to add the residue, use the “insertResidue” command. I’ve provided the commands for inserting a tryptophan below (just put your structure in last.1.pdb). Also, are you using MMB 2.13?  This probably won’t work with earlier revisions.  Also, could you post such questions on the MMB forum on simtk.org, or to the rnatoolbox-help at simtk.org list? Can we put this one there? That way others will benefit.

firstStage 2
lastStage 2
loadSequencesFromPdb
insertResidue A 49 W

I sent you an email some months ago about a new feature that constrains backbone dihedrals on one stretch of residues to be identical to that on another stretch. Is that still something you want to use?

Sam 

> 
> firstStage 2    
> lastStage 2   
> reportingInterval 1    
> numReportingIntervals  2
> 
> temperature 1.0
> #                   0         10        20        30        40        50        60        70        80        90
> #                   |         |         |         |         |        i|         |         |         |         |
> protein A 2           STPADVKEHPNSYVFMVDMPGVKSGDIKVQVEDENVLLISGERKREEEKEGVKYLKMERRIGKLMRKFVLPENANIEAISAISQDGVLTVTVN
> protein B 2           STPADVKEHPNSYVFMVDMPGVKSGDIKVQVEDENVLLISGERKREEEKEGVKYLKMERRIGKLMRKFVLPENANIEAISAISQDGVLTVTVN
> 
> mobilizer Rigid A 2 47
> mobilizer Rigid A 52 94
> 
> mobilizer Rigid B 2 47
> mobilizer Rigid B 52 94
> 
> constraint A 2 weld B 2
> 
> contact AllHeavyAtomSterics        A 2 94
> contact AllHeavyAtomSterics        B 2 94
> 
> 
> Kind regards,
> Erik
> 
> 
> Erik Marklund, PhD
> Postdoctoral Research Associate
> 
> Department of Chemistry
> Physical & Theoretical Chemistry Laboratory
> University of Oxford
> South Parks Road
> Oxford
> OX1 3QZ
> 

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