[Xplor-nih] rna database potential refinement

[Gokul Ramaswami]

Hi John,

Here is the output I get :

Powell::step: irregular exit: Line search abandoned: gradient may be incorrect
*-- POWELL ------ step=     20 --- stepsize=   0.01000 --- energy 
evals=   60 -*
|   E(poten)= -1547.2976913       grad=     6.3938934      ANGL=   
342.4001843 |
|       BOND=    15.9849558       CDIH=    12.8295295      IMPR=     
5.8861335 |
|       ORIE=  -583.0114776       PLAN=    56.2931712      RAMA= 
-1690.4008379 |
|        VDW=    11.8511017        noe=   280.8695484

I want it to do 2000 steps of cartesian minimization, but it quits 
after only 20-50.  I have been using the same force constants as in the 
rna_refi example.  Maybe my rama/orie terms have too much force?

Thanks,

Gokul

Quoting John Kuszewski <johnk at mail.nih.gov>:

> Hi Gokul,
>
> Could you send me the relevant output?
>
> Most likely, it just means that the minimizer got stuck.  The  
> gradients from the orie and rama terms are approximate, because  
> they're coming from databases of known structures, and so they can  
> occasionally be too rough for the minimizer.
>
> If all the experimental terms (NOE, RDC, etc) have acceptable  
> agreements, then you can probably take the final coordinates from  
> your rama + orie structures as converged.
>
> --JK
>
> On Mar 3, 2008, at 12:33 PM, Gokul Ramaswami wrote:
>
>> Hello Xplor users,
>>
>> I am trying to refine an rna molecule using the rama and orie database
>> potentials.  The problem is during the final minimization I get an
>> error message stating that the gradient may be incorrect and the
>> program terminates.  If I take out these 2 potentials, then the
>> minimization occurs without error, but the structure has poor base
>> stacking.  Any help would be greatly appreciated.
>>
>> Thanks,
>>
>> Gokul
>> _______________________________________________
>> Xplor-nih mailing list
>> Xplor-nih at nmr.cit.nih.gov
>> http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
>
>
>
>