[AMBER] Amber calculate RMSF

From: <18xdwu.stu.edu.cn>
Date: Fri, 5 Nov 2021 00:29:51 +0000

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
No 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

Moving 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 Thu Nov 04 2021 - 18:00:02 PDT
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