RE: making new psf file from .prm and pdb file

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Tue Mar 05 2019 - 21:01:40 CST

Hi Hadi,

With the limited details you provided, and assuming your existing .psf and .pdb are simulatable with the parameters you have, couldn't you just make an atomselection in VMD and write out new files that only have the part of the structure you want to keep? Something like:

set keepsel [atomselect top "not (whatever you'd use to select the bad part)"]
$keepsel writepsf new.psf
$keepsel writepdb new.pdb

-Josh

On 2019-03-05 16:05:41-07:00 owner-namd-l_at_ks.uiuc.edu wrote:

Hello dear VMD users,
I have a psf and pdb file of an structure and also its parameter files. I do not have the topology file of that. I need to remove a part of pdb file, but at the same time, the psf file and pdb file should match each other. Does any body know how can I make a new psf file?
Thank you in advance
Hadi

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