tryu looking at your initial restraint energy. if too high.
make sure your initial structure matches your initial rmsd value.
On 10/18/07, gurpreet singh <gps.iitm.gmail.com> wrote:
> Thanks Carlos
>
> Yes, The job was killed in the beginning of the run
>
>
>
> With Regards
> Gurpreet
>
>
>
> On 10/18/07, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
> >
> > actually you do have restraints and a force constant.
> >
> > does it die at step 1 or later?
> >
> > On 10/17/07, gurpreet singh <gps.iitm.gmail.com> wrote:
> > > Hello Amber users
> > >
> > > I am using Amber 9 , I want to apply TMD on a inhibitor docked to my
> > > protein. While running the TMD I am getting the following error"
> > >
> > > Coordinate resetting (SHAKE) cannot be accomplished,
> > > deviation is too large
> > > NITER, NIT, LL, I and J are : 0 0 1620 3196 3197
> > >
> > > Note: This is usually a symptom of some deeper
> > > problem with the energetics of the system.
> > >
> > > Generally to recver from this problem reduction in the force constant ot
> > > time step is the good idea
> > > but here IN TMD I am not all using any restraints so what else is the
> reason
> > > for this.
> > >
> > > My input file :
> > >
> > > &cntrl
> > > imin = 0, ntx = 7, irest = 1,
> > > ntpr = 100, ntwx = 500, ntwe = 0,
> > > ntc = 2, ntf = 2,
> > > nstlim = 250000, dt = 0.002,
> > > tempi=300.0, temp0 = 300.0, ntt =1, tautp =2.0,
> > > ntb = 1, ntp = 0,cut=10.0,iwrap=1,ntr=0,
> > > itgtmd=1,tgtrmsd=11.11, tgtmdfrc=5.0, tgtrmsmask=":321",tgtfitmask=":
> > > 1-320.CA,C,N"
> > > &end
> > >
> > > &wt type='TGTRMSD', istep1 =0,istep2 = 50000,value1 = 11.11,
> > > value2 = 5.55, &end
> > > &wt type='TGTRMSD', istep1 =50001, istep2 = 250000,value1 = 5.55,
> > > value2 = 0.0, &end
> > > &wt type="END" &end
> > >
> > >
> > > here I am using such a high value of RMSD I dont know whether it is
> > > fissible or not. Suggest something.
> > >
> > >
> > > Thanks & Regards
> > >
> > > Gurpreet
> > >
> >
> >
> > --
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Received on Sun Oct 21 2007 - 06:07:25 PDT
