Solvation in VMD using Non Standard Solvent System

From: Babban Mia (
Date: Wed Aug 10 2011 - 07:35:32 CDT

Hello Everyone

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 ?

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)

Please advise ,Any help would be appreciated

Best regards

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