Thank you Viktor. Now I see what you mean. I need to think about it
again. Best! ---Shawn
----- Original Message -----
From: Viktor Hornak <hornak.csb.sunysb.edu>
Date: Friday, April 8, 2005 5:24 pm
Subject: Re: AMBER: question about TGMD: vlimit exceeded for step
> xhu1.memphis.edu wrote:
>
> >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
> >
> -----------------------> ???
> Shawn,
> I am not sure I understand what you're trying to do. Fitmask just
> specifies which parts of your molecule and reference you want to
> overlap
> _before_ RMSD on parts of molecule specified by rmsmask is
> calculated.
> If you change the way molecules overlap (i.e. by changing the
> fitmask)
> you change the relative position of those parts of the molecule
> that you
> calculate RMSD for and thus the TMD force will be different. If
> you
> 'apply TMD' only to residues 81-86 (i.e. you calculate RMSD for
> :81-86,
> which happens when your tgtrmsd is set to :81-86) and the rest of
> your
> system is free to move, then you're getting kind of random RMSD
> for
> :81-86 because your system can move/rotate relative to your
> reference.
> Maybe TMD is not the right tool for whatever you're trying to
achieve?
>
> Cheers,
> -Viktor
>
> >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.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.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
> >>>
> >>>
> >>>
> >
> >
> >------------------------------------------------------------------
> -----
> >The AMBER Mail Reflector
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> >
>
>
> --
> ===================================================================
> Viktor Hornak
> Center for Structural Biology Phone: (631)632-1439
> SUNY at Stony Brook Fax: (631)632-1555
> Stony Brook, NY 11794-5115 E-mail: viktor.hornak.sunysb.edu
> ===================================================================
>
> -------------------------------------------------------------------
> ----
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Received on Sat Apr 09 2005 - 00:53:00 PDT
