Generating PSF file from PDB

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Amirhossein Memari

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Nov 9, 2021, 2:12:07 PM11/9/21
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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

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Nov 9, 2021, 2:14:38 PM11/9/21
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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

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Nov 9, 2021, 2:33:53 PM11/9/21
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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

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Irfan Alibay

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Nov 9, 2021, 2:35:15 PM11/9/21
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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

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Nov 12, 2021, 8:57:03 AM11/12/21
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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

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Nov 12, 2021, 11:58:01 AM11/12/21
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Here is the link I forgot earlier:

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