From: Sebastian Wilhelm (Sebastian.Wilhelm_at_rwth-aachen.de)
Date: Sun Feb 20 2011 - 07:54:35 CST

Hi,

I have an error occurring while using Auto PSF Builder: the coordinates of
100 simple argon molecules which I simulated by DL POLY are converted by VMD
to a .pdb-file. Loading them and the topology file
top_all27_prot_lipid_na.inp into Auto PSF Builder and choosing 'everything'
in step 2, in step 3 only one chain segment is presented which has a first
atom number of 1 and a last atom number of 101 (to be found in 'edit
chains'). Clicking on 'create chains' produces an application error 'ERROR:
failed on end of segment MOLECULE DESTROYED BY FATAL ERROR'. In the command
box, there is written 'unknown residue type'.

 

My goal is to calculate all intermolecular energies by NAMDenergy for that I
need a .psf-file.

What can I do? Do I have to change the topology file, and when how?
Thanks for your help.

Best regards,
Sebastian Wilhelm