Xiaodong,
since you omit any mask in your rms fit commands, which means that all
atoms are used:
Are you sure that your trajectory just comprises the pure protein and
not any waters or ions? In that case imaging maybe yielded a sort of
different system and thus the rms-fit of all atoms
(protein+ions+solvent) resulted in a different overall structure: re-try
with an explicit atom mask for the two rms fit commands using the same
mask as in your atomicfluct command.
(Stripping water molecules *prior* to imaging via "strip :WAT" may
result in a much quicker execution time of cpptraj, since you do not
need the solvent for your analysis.)
Does this solve your problem?
Otherwise:
Is your protein composed of just a single chain or of multiple chains,
and did you run your simulation with iwrap = 1?
If you have multiple chains, it may be that the image command resulted
in something different than you expected. Did you check the imaged
trajectory visually?
Try printing out the rmsd values: Are there any immediate big jumps in
the graph signalling a (re)imaging problem?
If your protein trajectory just contains a single chain, no water, no
ions, and no other residues like ligands, then the behaviour you
describe seems strange (to me): imaging should produce just a
translated/rotated geometry for a covalent system, which you then fit
via the rms command again to the first structure, calculate the average
and then the fluctuations with respect to the average.
Regards,
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
On 11/07/2021 08:45 AM, 吴晓东 wrote:
> Dear all,
> I have a protein system that runs CMD in a water box with PBC. In this simulation, I looked at the trajectory file. The protein remained stable in the water box during the simulation process and did not run out of the water box. After running MD simulation, I want to analyze RMSF. I use the following input file to run with cpptraj.
> #rmsf.in
> parm prmtop
> trajin S38D.nc
> rms first
> average crdset MyAvg
> run
> rms ref MyAvg
> atomicfluct byres out S38D-old.rmsf :1-486.C,CA,N
>
> Then, I want to see how RMSF will change if the protein is moved to the center of the water box. I wrote a wrap. In file and put the protein back in the center of the water box.
> #wrap.in
> parm prmtop
> trajin S38D.nc
> trajout wrap-S38D trajectory
> image origin center familiar com :132
> go
>
> Based on the generated trajectory, I run the RMSF calculation again.
> #rmsf-new.in
> parm prmtop
> trajin wrap-S38D
> rms first
> average crdset MyAvg
> run
> rms ref MyAvg
> atomicfluct byres out S38D-old.rmsf :1-486.C,CA,N
>
> It is puzzling that the protein is always in the water box whether it is moved to the center of the water box or not. So, I think the calculated RMSF should be consistent. However, the results of RMSF under these two conditions are very different. I don't know why?
> The results are as follows：
> ①No moving protein：
> #Res AtomicFlx
> 1.000 3.1073
> 2.000 2.9562
> 3.000 2.8570
> 4.000 2.9493
> 5.000 2.9838
> 6.000 3.0734
> 7.000 3.1263
> 8.000 3.1998
> 9.000 3.2446
> 10.000 3.2964
> 11.000 3.3608
> 12.000 3.4335
> 13.000 3.5786
> 14.000 3.5121
> 15.000 3.5382
> 16.000 3.5242
> 17.000 3.5047
> 18.000 3.6473
> 19.000 3.7766
> 20.000 3.9167
> 21.000 4.0491
> 22.000 4.2176
> 23.000 4.2456
> 24.000 4.0436
>
> ②Moving protein：
> #Res AtomicFlx
> 1.000 1.7617
> 2.000 1.4648
> 3.000 1.1541
> 4.000 1.1855
> 5.000 1.0084
> 6.000 0.9336
> 7.000 0.9189
> 8.000 0.9765
> 9.000 1.0182
> 10.000 1.1047
> 11.000 1.2287
> 12.000 1.4049
> 13.000 1.4985
> 14.000 1.3945
> 15.000 1.3098
> 16.000 1.2191
> 17.000 1.1698
> 18.000 1.2880
> 19.000 1.4401
> 20.000 1.6805
> 21.000 1.9415
> 22.000 1.9977
> 23.000 1.9622
> 24.000 1.7602
>
> It can be seen that the results are quite different, but I don't know why? In addition, can amber automatically handle periodic boundary conditions when calculating RMSF? When some residues of the protein run out of the water box, should I move the protein back to the center of the water box?
>
> I really hope to get an answer.
>
> Best,
> Xiaodong
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Received on Sun Nov 07 2021 - 14:00:02 PST
