From: Joshua Adelman (jla65_at_pitt.edu)
Date: Mon Oct 26 2009 - 20:03:37 CDT

I was wondering if anyone else has seen this happen and has a
solution. I'm attempting to solvate a small dipeptide molecule that I
constructed with Molefacture (single amino acid created with Protein
Builder and then ACE and CT3 terminal patches with autopsfgen). When I
attempt to solvate it with the Solvate-GUI, the output has the solute
atoms collapsed to the origin. The warning I get when the GUI is
loading the temporarily file after rotation, is:

Warning: failed to set coordinate for atom CD LYS:1
no segment

for all of the peptide atoms. The same error occurs when I just read
the auto_psf file of the solute without rotation. AUTO_PSF seems to
build the molecule correctly (the solute has a segid = P1). I'm
running VMD 1.8.7 (os x intel binary).

Josh