[AMBER] Fwd: Why RMSD goes fast to 5 angstrom?

From: Shulin Zhuang <shulin.zhuang.gmail.com>
Date: Wed, 18 Apr 2012 11:14:04 +0800

Hi, Aron,

Great thanks for rapid help.

The PDB ID of the crystal structure is 2H79, which is a crystal sructure of
human TR alpha bound T3 in *orthorhombic space group. *For this complex it
also have another cyrstal strucutre WITH pdb id:2H77, which is the crystal
structure of human TR alpha bound T3 in *monoclinic space group*. I
choosed the complex in *orthorhombic space group. *The* amber 03
forcefield*and the
*TIP3P water* box was applied. Is it due to the *orthorhombic space
group? *

For the rmsd calculating, I use ptraj:*

*ptraj com.prmtop << EOF
trajin npt1.mdcrd
trajin npt2.mdcrd
trajin npt3.mdcrd
reference minimized.pdb
center :1-268 origin mass
image origin center familiar
rms reference out 1CArmsd.out :1-267.CA
atomicfluct out bfactor.out .CA byres bfactor*

*I superimpose different conformations using VMD and found that the N
termini changed much and the loops also changed.

Best regards
Shulin
*
*
On Wed, Apr 18, 2012 at 10:40 AM, Aron Broom <broomsday.gmail.com> wrote:

> First, are you calculating the RMSD with a method that allows you to first
> align the backbone? If not, your RMSD will incorporate deviations due to
> translations and rotations, although I suspect that is not the case here.
>
> This simply seems like your crystal structure is not an accurate model for
> the solution structure, or at least, not an accurate model for the solution
> structure as defined by the forcefield you are using. Which forcefield are
> you using? Which water model? Are you certain that your parameters are
> appropriate for those models?
>
> Also, if you just watch the trajectory (in VMD for instance) how does it
> look? An RMSD of 5A could easily be caused by a single strand or loop or
> something that is not behaving in a well structured manner. Moreover, it
> may be that in reality it doesn't behave that way, but the dense packing in
> the crystal, and low temperature of X-ray diffraction have made that region
> appear rigid.
>
> I think there is a tutorial for VMD, that you might have to access through
> the NAMD website, that will guide you through assigning RMSDs on a
> per-residue basis. You could do that and then colour the structure
> accordingly and see which regions are contributing to the high RMSD.
>
> Finally, depending on the size of your protein and the quality of the
> crystal (1.9 angstroms resolution is decent, but not amazing) it simply
> might take more than 11ns to reach a stable structure from the possibly
> inaccurate starting point.
>
> ~Aron
>
> On Tue, Apr 17, 2012 at 10:26 PM, Shulin Zhuang <shulin.zhuang.gmail.com>wrote:
>
>> Dear All,
>>
>> I have routinely performed a 11 ns MD simulation in NPT ensemble based on
>> X-ray crystal structure with a resolution of 1.87 angstrom . After the
>> RMSD
>> analysis, I found that the C alpha RMSD is continiously increasing and
>> finally is is up to *5 *. The averaged RMSD for the* 0-1ns*
>> simulation, *
>> 1-6ns* simulation, *6-11ns* simulation is *2.3** , 2.86 , 3.89
>> ,*respectively. Attached
>> is the RMSD figures.* It seems abnormal* and could you tell me where is
>> the
>>
>> problem.
>>
>> The simulatioin input files were listed as following:
>> *
>> Minimization step 1 input:*
>>
>>
>> restrained mimimization
>>
>> &cntrl
>>
>> imin=1, maxcyc=1000, ncyc=500, cut=10.0, ntb=1,
>>
>> ntr=1, restraintmask='(:268) & (!.H=)', restraint_wt=10.0
>>
>> # here 268 is the ligand. In this step, the ligand and non-hydrogen part
>> of
>> the system were restrained.
>>
>> /
>>
>> *Minimization step 2 input:*
>>
>>
>> restrained mimimization
>>
>> &cntrl
>>
>> imin=1,maxcyc=1000, ncyc=500, cut=10.0, ntb=1, ntr=0,
>>
>> /
>>
>> *Heating stage input:*
>>
>>
>> restrained heating process
>>
>> &cntrl
>>
>> imin=0, irest = 0, ntx = 1, ntb = 1, ntr = 1, ntc= 2, tempi =
>> 0.0,
>> temp0 = 300.0,
>>
>> ntt = 3, gamma_ln = 1.0, nstlim = 25000, dt = 0.002, ntpr = 100, ntwx
>> = 500, ntwr = 500,
>>
>> cut=10.0, restraintmask='(:268) & (!.H=)', restraint_wt=5.0,
>>
>> ******
>>
>> */*
>>
>> *
>> *
>>
>> *1ns equilibration input:*
>>
>>
>> &cntrl
>>
>> ntx =7, ntr = 0, irest = 1, imin = 0, nrespa = 1, ntb =2, ntp=1,
>>
>> tempi =300.0, temp0 =300.0,cut=10.0, nstlim =500000, dt= 0.002,
>> ntpr=200,
>>
>> ntc=2, ntf=2, taup = 2, pres0 = 1.0, ntwr=500, ntwx=500, ntt=3,
>> gamma_ln=1.0,
>>
>> *5ns equilibration input:*
>>
>>
>> &cntrl
>>
>> ntx =5, ntr = 0, irest = 1, imin = 0, nrespa = 1, ntb =2, ntp=1, tempi
>> =300.0,
>>
>> temp0 =300.0,cut=10.0, nstlim =2500000, dt= 0.002, ntpr=200, ntc=2,
>> ntf=2, taup = 2, pres0 = 1.0,
>>
>> ntwr=500, ntwx=500, ntt=3, gamma_ln=1.0,
>>
>> *5ns equilibration input:*
>>
>> &cntrl
>> ntx =5, ntr = 0, irest = 1, imin = 0, nrespa = 1, ntb =2, ntp=1,
>> tempi =300.0, temp0 =300.0,cut=10.0, nstlim =2500000, dt= 0.002,
>> ntpr=200,
>> ntc=2, ntf=2, taup = 2, pres0 = 1.0, ntwr=500, ntwx=500, ntt=3,
>> gamma_ln=1.0,
>> /
>>
>>
>> Much appreciated to your help!
>>
>> Shulin
>>
>> _______________________________________________
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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
>
>
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Received on Tue Apr 17 2012 - 20:30:04 PDT
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