AMBER Archive (2007)

Subject: Re: AMBER: error while Running TMD

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Oct 17 2007 - 13:50:45 CDT

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_at_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_at_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_at_gmail.com
Stony Brook, NY 11794-5115          Web: http://comp.chem.sunysb.edu
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