From: Geist, Norman (
Date: Thu Apr 14 2022 - 00:42:06 CDT

Hi Sarbajit,

you can easily extract the system as a PSF/PDB file pair without water
from VMD and than resolvate your desired solvent. Eg:

set a [atomselect top "not water"]
$a writepsd my.psf
$a writepdb my.pdb

Than loads psf and pdb (in that order) and use the solvate plugin.
However, you might have to prepare the required files (TIP4P solvent
box) for the solvate plugin.

Alternatively, you can try retyping your system with CHARMM-GUI
(without water) and solvate there.


Am Mittwoch, den 13-04-2022 um 17:31 schrieb SARBAJIT LAYEK:

Dear NAMD experts,

I have a system with a carbon nanomaterial, an unfolded protein, and
water (TIP3P). I have the .psf file, but unfortunately, the topology
created long ago is lost. 

I would like to change the water model to TIP4P/2005. Can you suggest
how to do this for every water molecule in the previous system (in the
absence of the topology file)?

Thanks in advance.
Sarbajit Layek
(junior research fellow)

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