AMBER Archive (2005)

Subject: Re: AMBER: question about TGMD: vlimit exceeded for step

From: xhu1_at_memphis.edu
Date: Fri Apr 08 2005 - 16:55:05 CDT

Thank you very much, Vikror. But I am confused. Maybe I didn't make
myself clear in my last email: the overall RMSD(residue 3-122) between
the initial structure and the reference structure is 4.345, so I set
tgtrmsd=4.435. now I want to apply targeted MD at residue 81-86, all
the other is free to move, then see if the simulated structure
achieves the reference structure or not at the end. By this,I can
judge if the residues 81-86 play as a key in this sturcuture change.
after reading your reply, besides switching the maskes, I also need to
change the tgtrmsd value. this value should be the RMSD of residue 81-
86 between the initail and the reference structure, am I right? Thanks
again

Shawn

----- Original Message -----
From: Viktor Hornak <hornak_at_csb.sunysb.edu>
Date: Friday, April 8, 2005 3:47 pm
Subject: Re: AMBER: question about TGMD: vlimit exceeded for step

>
> I think your masks are reversed. According to your input you
> overlap
> your molecule to a reference by residues 81-86 and calculate the
> force
> based on RMSD of residues 3-122. You should try to switch the
> masks,
> such as: tgtfitmask=':3-122', tgtrmsmask=':81-86 & !@H=', or use
> positional restraints (ntr=1) for atoms :3-80,87-122
> (restraintmask=':3-80,87-122', restraint_wt = 2.0, or such) and
> use
> targeted md for :81-86 (tgtrmsmask=':81-86')...
>
> Cheers,
> -Viktor
>
> xhu1_at_memphis.edu wrote:
>
> >Dear all,
> >
> >I am trying to run TGMD for a system: a 124-residue protein in a
> >waterbox.
> >
> >Using AMBER7, weighted TGTRMSD from 4.345 to 0, TGTMDMDFRC=10 or
> 5 or
> >1, restrain force applied on residue 3-122, job running OK. then
> I
> >tried to apply the restraint force on residue 81-86 only, to see
> if
> >the structure will go to the reference structure as well. AMBER7
> seems
> >not be able to do this. I move to AMBER8. Here is the input file:
> >*****************************************************************
> >#Data collection at 298K
> > &cntrl
> > IMIN = 0,ntx=5,irest=1,
> > ntpr=10, ntwr=500,
> > ntb=1,ntr=0,
> > ntf=2,ntc=2,
> > cut=8.5, nscm = 1000,
> > NSTLIM = 400000, DT = 0.002,
> > NTWX=500, NTWV=500,NTWE=500,
> > TEMP0 = 298.0, TEMPI=298.0, NTT=1, TAUTP=2.0,
> > nmropt=1, itgtmd=1, tgtrmsd=4.345, tgtmdfrc=10.00,
> > tgtrmsmask=":3-122", tgtfitmask=":81-86 & !@H=",
> > &end
> > &wt
> > TYPE='TGTRMSD', istep1 =0, istep2 = 200000,
> > value1 = 4.345, value2 = 0.3,
> > &end
> > &wt
> > TYPE='TGTRMSD', istep1 =200001, istep2 = 400000,
> > value1 = 0.3, value2 = 0.,
> > &end
> > &wt
> > type="END",
> > &end
> > &rst
> > iat(1)=0,
> > &end
> >END
>
>**********************************************************************
*
> >
> >I got a problem: job stopped immediately, and gave the informatin
> as
> >following:
> >
> >*********************************************
> >
> > NSTEP = 10 TIME(PS) = 360.020 TEMP(K) = 5403.88
> PRESS
> >= 0.0
> > Etot = 867849.0298 EKtot = 181470.7791 EPtot =
>
> >686378.2507
> > BOND = 1342.9958 ANGLE = 1534.9087 DIHED =
>
> >1235.1722
> > 1-4 NB = 1138.3272 1-4 EEL = 5449.3066 VDWAALS =
>
> >9292.6310
> > EELEC = -64101.8524 EHBOND = 0.0000 RESTRAINT =
>
> >730486.7616
> > EAMBER (non-restraint) = -44108.5108
> > Ewald error estimate: 0.2247E-04
> >Current RMSD from reference: 13.246
> >Current target RMSD: 4.345
> > -----------------------------------------------------------------
> -----
> >
> > NMR restraints: Bond = 0.000 Angle = 0.000 Torsion =
>
> >0.000
>
>======================================================================
=
> > vlimit exceeded for step 11 ; vmax = 21.4771801052079
> > vlimit exceeded for step 12 ; vmax = 1952.41027295489
> >
> > Coordinate resetting (SHAKE) cannot be accomplished,
> > deviation is too large
> > NITER, NIT, LL, I and J are : 0 2 439 882 883
> >
> > Note: This is usually a symptom of some deeper
> > problem with the energetics of the system.
>
>**********************************************************************
*
> >
> >I noticed that the "Current RMSD from reference" is huge
> different
> >from the "Current target RMSD". Is my TGTMDFRC too large?? I
> decreased
> >this value to 5, then 1, after running several tens steps, jobs
> >stopped for the same reason too. I read some emails in the
> mailing
> >list. the value of TGTMDFRC between 1-5 or 1-10 should be OK.
> then
> >does my input file have a problem?
> >
> >Thank you very much for your help!
> >
> >Shawn
> >
> >

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