Re: Solvation in VMD using Non Standard Solvent System

From: Axel Kohlmeyer (
Date: Wed Aug 10 2011 - 07:47:35 CDT

On Wed, Aug 10, 2011 at 8:35 AM, Babban Mia <> wrote:
> Hello Everyone

fist off, please avoid cross-posting to multiple mailing lists.
your question is about VMD, so you should simply post
to the VMD list. thanks.

> I am solvating my protein using a non standard solvent system but I am
> getting an error which says :
> First query error :
> reading structure from psf file /Users/babban/Desktop/unit.psf
> Unable to add (duplicate?) residue U:1
> "unit.psf is the psf file for the solvation box that I have created "
> Any idea on what might cause this error ?

inconsistent naming of residues and their residue id?
does your psf file have unique residue ids for each residue?

> Second query:
> I have pdb/psf of my peptide and similarly I have pdb/psf of my solvent box
> and I am uploading them in the GUI of solvation console in VMD even though
> the size of solvent box is set ,the GUI is insisting on putting the min/max
> values for the box(which I already have a PDB/PSF for)

because the solvate plugin will replicate the solvent box as needed
in case you need a larger solvation box than what your solvent box


> Please advise ,Any help would be appreciated
> Best regards
> Babban

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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