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
>>>
>>>
>>>
>
>
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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 Fri Apr 08 2005 - 23:53:00 PDT
