Re: ERROR: Molecule destroyed by fatal error

From: Axel Kohlmeyer (
Date: Mon Jan 27 2014 - 13:37:58 CST

On Mon, Jan 27, 2014 at 2:31 PM, Marlet Martinez <> wrote:
> Hello All,
> I am trying to generate a .psf of a protein and a molecule inside the pocket
> (ligand) however when I run the .tcl script I got this error:
> error: segid ligand is longer than 4 characters allowed by psf format
> ERROR: failed on writing structure to psf file
> Effectively the .psf was not generated and when I checked the .pdb the
> ligand is broken.
> Thanks a lot for your attention and I would appreciate any suggestion
> regarding this issue,

how about the suggestion that is implied by the error message, i.e. to
use a segment id that has no more than 4 characters?


> Marlet

Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.

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