VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Mon Oct 26 2009 - 21:31:23 CDT

Hi Josh,
I have followed the procedure that you outlined but was unable to
reproduce the bug (although I'm not running osx). Could you please email
me (off list) the psf and pdb files that you use as input to solvate,
and the console output generated as solvate runs?
Thanks,
Peter

Joshua Adelman wrote:
> 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
>
>
>
>