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
> >
>
>
> --
> ===================================================================
> Carlos L. Simmerling, Ph.D.
> Associate Professor Phone: (631) 632-1336
> Center for Structural Biology Fax: (631) 632-1555
> CMM Bldg, Room G80
> Stony Brook University E-mail: carlos.simmerling.gmail.com
> Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
> ===================================================================
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Received on Sun Oct 21 2007 - 06:07:21 PDT
