Generating PSF file from PDB

Skip to first unread message

Amirhossein Memari

Nov 9, 2021, 2:12:07 PM11/9/21
to MDnalysis discussion
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 

Irfan Alibay

Nov 9, 2021, 2:14:38 PM11/9/21
to MDnalysis discussion

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,


Amirhossein Memari

Nov 9, 2021, 2:33:53 PM11/9/21
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
You received this message because you are subscribed to the Google Groups "MDnalysis discussion" group.
To unsubscribe from this group and stop receiving emails from it, send an email to
To view this discussion on the web visit

Irfan Alibay

Nov 9, 2021, 2:35:15 PM11/9/21
to MDnalysis discussion
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?

Nov 12, 2021, 8:57:03 AM11/12/21
to MDnalysis discussion
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.

V Joe Klimkowski

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

Reply all
Reply to author
0 new messages