Convert dcd and pdb to .np and .parm7 file

[TianmingQu]

Dear all, How can I convert the dcd and pdb file to the .np and .parm7 file I need to use in pytraj?

[hainm]

Why don’t you just load dcd and pdb directly?

[TianmingQu]

Oh, I really thought I have to convert. Because i want to do pca analysis and I saw your example says it needs to use the np and parm7 files😨

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发件人: Hai Nguyen @.> 发送时间: Friday, October 8, 2021 4:22:39 PM 收件人: Amber-MD/pytraj @.> 抄送: Tianming Qu @.>; Author @.> 主题: Re: [Amber-MD/pytraj] Convert dcd and pdb to .np and .parm7 file (#1582)

Why don’t you just load dcd and pdb directly?

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[TianmingQu]

So how can I load dcd and pdb file directly?

[hai-schrodinger]

So how can I load dcd and pdb file directly?

Just like you would load with .nc and .parm7 files.

traj = pt.load('your.dcd', top='your.pdb')

[TianmingQu]

Thanks! So then I can follow the instructions to do pca analysis with this dcd file directly, is this correct?

[hai-schrodinger]

Yes.

[TianmingQu]

It says: "RuntimeError: n_atoms = 0: make sure to load correct Topology filename or load supported topology (pdb, amber parm, psf, ...)"😭

[hai-schrodinger]

do you have .psf file? use it instread of .pdb. I am sure that pytraj (cpptraj under the hood) works well with .dcd file format.

[TianmingQu]

I have several .psf file download from charmm-gui, should I use the step1_pdbreader.psf?

[hai-schrodinger]

Just give it a try, I don't know much about charmm.

[TianmingQu]

So is there any output for all the vectors? Based on my understanding on PCA there should be a vector on every Ca atom, right? I mean if I choose Ca to do the PCA analysis?

[hai-schrodinger]

So is there any output for all the vectors? Based on my understanding on PCA there should be a vector on every Ca atom, right? I mean if I choose Ca to do the PCA analysis?

Please see the docs: https://amber-md.github.io/pytraj/latest/_api/pytraj.all_actions.html?highlight=pca#pytraj.all_actions.pca

[TianmingQu]

So according to this doc, should set n_vecs = -1, correct?

[TianmingQu]

Also another question is that, can pytraj be used to do cavity volume analysis in protein MD simulation? Sorry for my so many questions😰

[hai-schrodinger]

Also another question is that, can pytraj be used to do cavity volume analysis in protein MD simulation? Sorry for my so many questions😰

I don't think so. Alternatively, you can use mdanalysis or mdtraj to see if they can.

[TianmingQu]

Thanks again! Then do you know is there anyway I can use VMD to visualize these vectors?

[hai-schrodinger]

I am sorry I don't know. May be try to understand the format and write the raw array to that format?

[TianmingQu]

Thank you! You've helped a lot!

[drroe]

Thanks again! Then do you know is there anyway I can use VMD to visualize these vectors?

You can use the nmwiz and related keywords for the diagmatrix command in CPPTRAJ (not sure if pytraj has access to this but it might). This will output files in a format that can be read by the NMWIZ plugin for VMD which is used to visualize eigenvectors. I haven't tested it in a while but it should still work.

[TianmingQu]

Sounds cool @drroe ! Is there any examples that I can take a look about how to use it?

[hainm]

Sounds cool @drroe ! Is there any examples that I can take a look about how to use it?

https://amberhub.chpc.utah.edu/introduction-to-principal-component-analysis/

(PS: I got that from google search "nmwiz cpptraj")

[TianmingQu]

Hi, is pytraj available to do RMSF analysis?

[hai-schrodinger]

Hi, is pytraj available to do RMSF analysis?

Hi, yes. Please see: https://amber-md.github.io/pytraj/latest/_api/pytraj.all_actions.html#pytraj.all_actions.atomicfluct

Please see that page for other types of analysis too. Cheers.