running multiple analysis in single file question

[groponp]

Dear, I want to do multiple analysis using an only script, but I have doubt , I show my script below:

parm name.psf 
trajin namd_fixpbcb.dcd   # it is the traj without pbc effect produced with autoimage 

rmsd  first :@CA&!(:WAT|:LIG) out rmsd.dat 
atomicfluct  irst :@CA&!(:WAT|:LIG) out rmsf.dat
hbond 
distance  
run

Q1: Is my command from rmsd rigth? Q2: How do I generate the PDB from atomicfluct to be colored by bfactor? Q3: The rmsd fit affect the folowing analysis? Q4: Is in atomicfluct the fit task done automatic?

[drroe]

Q1: Is my command from rmsd rigth?

If what you want is CA best-fit coordinate RMSD using the first frame as a reference, excluding WAT and LIG residues, then yes.

Q2: How do I generate the PDB from atomicfluct to be colored by bfactor?

You need to specify the bfactor keyword for atomicfluct, then specify that data to the output PDB with bfacdata. You also need to pick what you want to use as the coordinates; could be the average, first frame, etc. So for example, this input will put calculated B-factors into a PDB:

parm ../tz2.parm7
trajin ../tz2.nc
atomicfluct A0 :2-12
average crdset MyAvg
run
crdout MyAvg fluct.2.pdb bfacdata A0 chainid " "

Q3: The rmsd fit affect the folowing analysis?

Yes, if you're doing best-fit RMSD then the coordinates are affected for all following actions.

Q4: Is in atomicfluct the fit task done automatic?

No, so in your case you are best-fitting to the first frame as your reference for the atomicfluct calculation. Check all the output that CPPTRAJ produces. I also highly recommend reading the manual entries on all of these commands/keywords.

[groponp]

Thanks so much for you anwser !

[drroe]

If this issue isn't actually resolved, please do reopen it!

[groponp]

This is resolve!