[RNABuilder-help] Re: R: Re: R: Re: ions

[Samuel Flores]

> Before your e-mail, I have tried to equalize the order number of atoms of the target and model pdb.

This may not matter.  RNABuilder will try to guess the positions of any missing atoms.

> I have fixed the problem for His31, but there was still some problem with Iso35. Now I try to discard this residue which is not fundamental for the animation..
> 

What is ISO?  maybe try substituting a canonical amino acid.  we don't support non-canonical residues.

> I have a question...Last.2.pdb is produced from the data obtained by the fitting with last.1.pdb?

sort of.  If you look at trajectory.2.pdb, the first frame of that trajectory should superimpose almost perfectly on last.1.pdb.  Then the dynamics will run for a while, and the last frame of trajectory.2.pdb is the same as last.2.pdb.

The internal coordinates at the beginning of stage 2 are matched to last.1.pdb.  So one more thing you can try is adding the following parameter:

matchIdealized true

this will set the bond lengths and angles to their default (idealized) values.  Only the torsion angles will vary, for most residues.  Not sure if this will fix your problem though.

please send such questions to rnatoolbox-help

Sam  
  


> 
> Matteo
> 
> Il 24/01/11, Samuel Flores <samuelfloresc at gmail.com> ha scritto:
>> 
>> Perhaps the problem is with the structures you started with?  in last.1.pdb?
>> 
>> 
>> You can delete the side chain atoms from last.1.pdb and let RNABuilder guess at their positions, which might fix the issue.
>> 
>> I looked at the files you sent last time and they seem fine.  If the above doesn't work you can send me your last.1.pdb and contacts.dat again and I'll take a look.
>> 
>> 
>> Sam
>> 
>> On Jan 24, 2011, at 9:42 AM, Matteo Maria Colombo wrote:
>> 
>>> Hi Samuel, I was ill all the weekend...now I'm better
>>> 
>>> The ions seem to be almost ok, but the main problem now is about the residue His31, where the atoms bond are completely crazy...I've observed that in the two PDB (model and target) there is some difference in the number order of the atoms...could it be an explanation?
>>> 
>>> Matteo
>>> 
>>> Il 22/01/11, Samuel Flores <samuelfloresc at gmail.com <samuelfloresc at gmail.com>> ha scritto:
>>>> 
>>>> how did things go with the ion locations?
>>>> 
>>>> 
>>>>> Hi Samuel, these are the files...
>>>>> 
>>>>> There are two main troubles:
>>>>> 
>>>>> 1- The ions that cannot move (and i can see only one of the two I have defined)
>>>>> 
>>>>> 2- The contacts between the residues are not well defined.
>>>>> 
>>>>> I have tried to follow the tutorial, but I am not super familiar with program building and sure there will something that I have made wrong...
>>>>> 
>>>>> Thank you very much for your availability!
>>>>> 
>>>>> Matteo
>>>>> <contacts.protein-morphing_mg4.dat><catB-hex-mg.pdb><catB-cd4-mg.pdb>
>>>> 
>> 

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