On Wed, Dec 15, 2010, Rossella Noschese wrote:
> well, I mean that j value never reaches the target and it gives a large
> penalty and a deviation from the target torsion value.
>
>
> H VAL 2 -- HA VAL 2: 7.685 7.600 0.085 0.036 j
> H ILE 7 -- HA ILE 7: 9.100 8.100 1.000 5.000 j
>
>
>
>
> this is the result of LISTIN:
> (it seems to me to be ok,isn't it?)
>
> ******
> H ( 8)-N ( 7)-CA ( 9)-HA ( 10) NSTEP1= 0 NSTEP2= 0
> R1 = 6.400 R2 = 7.400 R3 = 7.600 R4 = 8.600 RK2 = 5.000 RK3 = 5.000
> Rcurr: 9.554 Rcurr-(R2+R3)/2: 2.054 MIN(Rcurr-R2,Rcurr-R3): 1.954
> ******
> H ( 80)-N ( 79)-CA ( 81)-HA ( 82) NSTEP1= 0 NSTEP2= 0
> R1 = 6.900 R2 = 7.900 R3 = 8.100 R4 = 9.100 RK2 = 5.000 RK3 = 5.000
> Rcurr: 9.451 Rcurr-(R2+R3)/2: 1.451 MIN(Rcurr-R2,Rcurr-R3): 1.351
Everything looks OK that I see. You could try a really small peptide (say
just ILE by itself) and see if the J-restraints seem to work. There could be
some competing energy terms or restraints in the full peptide that prevent the
phi angle from reaching the desired value.
...dac
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Received on Wed Dec 15 2010 - 09:00:03 PST
