[gmx-users] g_rmsf fitting

[tangxuan]

Hi Tsjerk,
Yes, you are right. My protein has multiple subunits.  I have a original 
tpr file ref1.tpr which is the input to start the simulation. I have 
checked the protein structure
in this tpr file. The subunits have no contact each other obviously, 
without jump in them and I can not see an intact protein. However, the 
structure in the frames  shows that there is a whole protein with jump.
Therefore, the structure in the tpr file is different from the structure 
in the first frame. 
The simulation is 30ns long and I am trying to calculate the rmsf 
between 20ns and 30ns. I removed the jumps in whole simulation(trjconv 
-f .xtc(.trr) -s ref1.tpr -pbc nojump) first and  got the nojump xtc 
file between 20ns and 30ns. The main difference between is the tpr file 
at 20ns(ref20.tpr) i used and two ways I have used to get it:
1)  used ref1.tpr and original trr file to get a tpr file at 20ns 
ref20.tpr by tpbconv.
2) used ref1.tpr and nojump trr file to get a tpr file at 20ns ref20.tpr 
by tpbconv.
then "g_rmsf -f .xtc (nojump) -s ref20.tpr   -res" is used to calculate 
the rmsf.
I take out part of the result below and the results are from two methods 
for same subunit.
1)
  62   0.1937
   63   0.2319
   64   0.2058
   65   0.2027
   66   0.1785
   67   0.1625
   68   0.1641
   69   0.1683
   70   0.1402
   71   0.1353
   72   0.1122
   73   0.0984
   74   0.0935
   75   0.1094
   76   0.0797
   77   0.1318
   78   0.0928
   79   0.1255
   80   0.1251
   81   0.1525
   82   0.1716
   83   0.1509
   84   0.1333
   85   0.0911
   86   0.0984
   87   0.0642
   88   0.0862
   89   0.0648
   90   0.0793
   91   0.0918
   92   0.1218
   93   0.1318
   94   0.1609
   95   0.1717
   96   0.1812
   97   0.1569
   98   0.1683
   99   0.1495 
  2)
  62   0.0843
   63   0.0946
   64   0.0801
   65   0.0652
   66   0.0801
   67   0.0605
   68   0.0728
   69   0.0733
   70   0.0561
   71   0.0559
   72   0.0628
   73   0.0552
   74   0.0613
   75   0.0758
   76   0.0639
   77   0.1172
   78   0.0677
   79   0.0877
   80   0.0981
   81   0.1313
   82   0.1490
   83   0.1460
   84   0.1133
   85   0.0947
   86   0.0761
   87   0.0602
   88   0.0677
   89   0.0587
   90   0.0530
   91   0.0545
   92   0.0647
   93   0.0451
   94   0.0560
   95   0.0541
   96   0.0572
   97   0.0486
   98   0.0535
   99   0.0459

Thanks

Tang
 
 
Tsjerk Wassenaar wrote:
> Hi Tang,
>
> It's just the general case of least-squares fitting:
>
> 1. Bring centres of geometry/mass to origin
> 2. Calculate (mass-weighted) rotation matrix
> 3. Rotate structure
> (4. Calculate squared displacements)
>
> But what do you mean with 'very different'. Can you provide an 
> example? What command line did you use? Do you have multiple subunits 
> and have jumps over PBC between the two reference structures?
>
> Cheers,
>
> Tsjerk
>
> On Jan 3, 2008 3:37 PM, tangxuan <tangxuan82 at gmail.com 
> <mailto:tangxuan82 at gmail.com>> wrote:
>
>     Hi,
>     Does anyone know how  fitting step works in detail when running
>     g_rmsf?
>     When I used two different tpr files with same protein structure but
>     different atoms position, the result is very different.
>     Can you explain this ?
>     many thanks!
>
>     Tang
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>
> -- 
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931    
> F: +31-30-2537623
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