Re: [AMBER] j-restrained peptide

From: Rossella Noschese <noschese.rossella.gmail.com>
Date: Wed, 15 Dec 2010 18:33:53 +0100

I'm trying with ACE ILE NHE and only its j-restraint. Actually it's still
running, but from the .info file I see energy restraint is still high.
While waiting....
Do you think it's possible that the rjcoeff I calculated (that really worked
well for VAL and that are directly related to the torsional angle from the j
value without need of passing through +60) give a torsional value that is
incoherent with the force field?


2010/12/15 case <case.biomaps.rutgers.edu>

> 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 - 10:00:04 PST
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