VMD-L Mailing List

From: Mohammad Elgamacy (mohammad.elgamacy_at_vub.ac.be)
Date: Wed Feb 13 2013 - 08:55:03 CST

Greetings,

I have been trying to combine the PSF's of a small molecule and a large hydrated lipid patch (512 POPC and more than 17000 water molecules) but I keep getting a read error as I try to load the hydrated patch's PSF unto VMD, as follows:

>Main< (cplx_setup) 9 % package require psfgen
  1.6
>Main< (cplx_setup) 10 % readpsf i_s.psf
  psfgen) reading structure from psf file i_s.psf
  psfgen) psf file does not contain cross-terms
>Main< (cplx_setup) 11 % readpsf popc512.psf
  psfgen) reading structure from psf file popc512.psf
  psfgen) Unable to add (duplicate?) residue TIP3:1000

  MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.

Do you have any idea why might this be happening and how can I get around it?

Thanks in advance,
Mohammad