Generating PSF file from PDB

[Amirhossein Memari]

hello guys 
I am new to MDAnalysis and I want to convert a pdb file into psf file and then neutralize the system.

Would you guide me in this path 

Thanks

[Irfan Alibay]

Hi,

Welcome to MDAnalysis!

As far as I am aware this cannot be done via MDAnalysis. Unfortunately MDAnalysis does not deal with writing / converting topology formats, we leave that to other libraries specialised in this (e.g. parmed).

Best regards,

Irfan

[Amirhossein Memari]

Thanks Irfan

Do you know any possible libraries that could do this? 

I try psfgen but when I install the package, I couldn't import it and I get the module error

Sent from my Huawei phone

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[Irfan Alibay]

I unfortunately wouldn't be much help here - I have used CHARMM-GUI for similar things, but it doesn't allow for programmatic access.

Maybe one of the other MDAnalysis users or developers might be able to pitch in here?

[vjo...@gmail.com]

It sounds like your effort to run psfgen is through VMD. That should not be a problem, but you can install psfgen & run it from the command line outside of VMD. Here is the specific UIUC psfgen website, along with a link to the User's Guide.

Best,

V Joe Klimkowski

[vjo...@gmail.com]

Here is the link I forgot earlier:

https://www.ks.uiuc.edu/Research/vmd/plugins/psfgen/