Re: [AMBER] Problems with RMSF calculations

From: <>
Date: Sat, 27 Jun 2020 12:56:05 -0700

   Hi Kenneth,

   Thanks for your suggestion! I tried to use the rms .CA first out rms.out to
   ensure that I am using the first frame as a reference and my results look
   exactly as the one from the older version of the cpptraj script (with
   reference ../../prod/pd1/ 1 statement ). The attached graph can show
   that it is identical to the one I send earlier.

   Hence my problem still remains. I don’t think cpptraj RMSF script is
   actually giving me the anticipated ‘average’ value of the RMSF when using
   two 250 ns simulations.

   I would appreciate any suggestions and explanations!

   Thanks a lot in advance,


   From: [1]Kenneth Huang
   Sent: 26 June 2020 14:50
   To: [2]AMBER Mailing List
   Subject: Re: [AMBER] Problems with RMSF calculations


   My guess is the it might not be fitting to to the first frame- you can try

   parm ../../prod/pd1/wt.prmtop

   trajin ../../prod/pd1/[1]wt_[2]

   trajin ../../prod/pd2/[3]wt_[4]

   rms .CA first out rms.out

   atomicfluct out RMSF.dat .CA byres

   Which should avoid any ambiguity of if it's fetching the wrong frame.



   On Fri, Jun 26, 2020 at 2:49 PM <> wrote:



> I have a total of 500 ns trajectory - 250 + 250 ns - starting from the

> same

> eq.rst file. I calculated the RMSF (wrt to the first frame as the

> reference)

> for this 500 ns using this cpptraj script:


> parm ../../prod/pd1/wt.prmtop

> trajin ../../prod/pd1/[1]wt_[2]

> trajin ../../prod/pd2/[3]wt_[4]

> reference ../../prod/pd1/[5]wt_[6] 1

> rms .CA reference

> atomicfluct out RMSF.dat .CA byres

> run



> I would expect the RMSF calculated using this script to give the

> RMSF from the two production runs but it seems that the RMSF calculated

> using the input above is not the true average of the two trajectories.



> The attached graph will make it clearer.

> comp_mean.png contains the RMSF calculated using cpptraj for the entire

> PD1

> and PD2 and for PD1 + PD2. I have also plotted here the mean RMSFs (for

> 10ns

> chunks) for PD 1 and PD 2 that I calculated using python. Am I using

> RMSF script incorrectly? I want to calculate the residue-wise

> fluctuations

> of the Ca atoms of the peptide backbone of my entire simulation (i.e.

> PD 1

> and 2 combined).



> Thanks a lot in advance for all the help!


> Kartik Lakshmi Rallapalli


> References


> 1.


> 2.

> 3.


> 4.

> 5.


> 6.

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(image/png attachment: RMSF.PNG)

Received on Sat Jun 27 2020 - 13:00:04 PDT
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