Re: [AMBER] about rms atomic fluctuation for protein crystal .thank you very much!

From: Pawel <>
Date: Mon, 14 Oct 2013 12:04:40 -0400

Hi Aimee,

Without seeing your data directly it is hard to tell what could be
happening. Having said that, a few comments,

1. Your general interpretation of Figure 8 referring to "bfac_lat" and
Figure 9 to "bfac_asu" is correct. However:

2. The script you are using was written after the paper
you are referring to, so the analysis is not directly comparable. In
particular, the "bfac_lat_calpha" in Figure 8 where calculated using a
different approach than the one used in BasicAnalysis. In general,
BasicAnalysis is still just a prototype, not documented, and requires
some work before an official release is made.

3. Before running make sure that in each frame of
your trajectory the center of mass of the entire supercell is exactly
aligned with the center of mass of the supercell produced from the
original PDB asymmetric unit coordinates (i.e. a supercell where one of
the asymmetric units has exactly the same coordinates as the PDB).

4. After, visually inspect the individual trajectories
in the revsym directory to see if they are aligned with the original
asymmetric unit. I usually add a frame to my trajectory which has the
supercell created from the original pdb coordinates. When you run, each of the asymmetric units from this frame should
align perfectly with the original PDB. If not, there is an error either
with how the centers of mass are being aligned or with how the symmetry
operations are being applied.

5. You mention "all atomic positions haven't rescaled at any steps. " If
you were running a constant pressure simulation you want to make sure
you are rescaling coordinates to account for fluctuations in the box
size at each step.

Hope these ideas point you in the right directions. Let us know if you
have questions,

On 10/14/2013 07:36 AM, Yongxiu Li wrote:
> Dear everyone,
> I want to construct the unit cell as the tutorial13 and do the
> same work as the David A. Case's paper "Simulations of a protein
> crystal with a high resolution X-ray structure: Evaluation of force
> fields and water models." /J. Phys. Chem. B/ *114*:12811-12824.
> Different from the paper, we construct the simulation Cell from 108
> individual unit cells
> in a 3*3*3 arrangement and simulate the system for 150ns using amber
> FF99SB force field and TIP3P water.
> After simulation, I use the '' script in
> AmberTools/src/xtalutil/Analysis to do each step analysis. Each step
> is the same as but all atomic positions haven't
> rescaled at any steps. After many steps' analysis, we use the
> '' to analyse the last 100ns bfactor . I understand
> that figure8 is the bfac_lat_calpha.dat in this script and figure9 is
> the bfac_asu_calpha.dat . I want to know whether I misunderstand to
> distinguish this two figure and their analysis script . Compared with
> figure8 in Case's paper,why the bfac_lat_calpha.dat which I gained is
> so big.
> the scipt is that :
> Because the paper said in figure9 the atomic fluctuations were
> computed on the basis of the distribution of each atom obtained after
> optimal quaternion alignments of the protein backbones. I do a little
> modification in ctraj_bfactor_asu(rms reference mass :1-64&!(.H=)
> changed to rms reference mass :1-64.CA,C,N).
> Best wishes!
> Aimee Li
> In the attachmet, amber-3-3-3.png is the bfactor. and figure 8 and
> figure9 are the pictures in Case's paper.
> next two script are using to compute the bfactor.
> ctraj_bfactor_asu:
> parm asu.prmtop
> trajin 25001 75000
> trajin 25001 75000
> ......
> trajin 25001 75000
> trajin RevSym 25001 75000
> reference AvgCoord_asu.rst7.1
> rms reference mass :1-64.CA,C,N
> atomicfluct out bfac_asu_calpha :1-64.CA byatom bfactor
> atomicfluct out bfac_asu_sdch :1-64&!(.H=,CA,C,O,N) byres bfactor
> atomicfluct out bfac_asu_bkbn :1-64.CA,C,N byres bfactor
> atomicfluct out bfac_asu_all :1-64 byres bfactor
> and ctraj_bfactor_lat:
> parm asu.prmtop
> trajin 25001 75000
> trajin 25001 75000
> ......
> trajin 25001 75000
> trajin RevSym 25001 75000
> atomicfluct out bfac_lat_calpha.dat :1-64.CA byatom bfactor
> atomicfluct out bfac_lat_sdch.dat :1-64&!(.H=,CA,C,O,N) byres bfactor
> atomicfluct out bfac_lat_bkbn.dat :1-64.CA,C,N byres bfactor
> atomicfluct out bfac_lat_all.dat :1-64 byres bfactor
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Received on Mon Oct 14 2013 - 09:30:02 PDT
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