VMD-L Mailing List

From: Tu.Le_at_csiro.au
Date: Mon May 02 2011 - 22:33:01 CDT

Hi,

I want to generate psf file for a cyclic peptide containing 7 amino acids.
I used the autopsf with 4 steps but did not get the right structure.

This was what I did:

After running step 2 and allocating the original pdb file, in the step 3 windows, a line automatically appear:
P1 7 1-109 NTER CTER Prot
I did not edit chain and continued with step 4 by adding patch: LINK A:7 A:1, I got psf and pdb files that include the unwanted NTER and CTER.

I am wondering if I need to add First none last none to this segment at step 3?

I really appreciate if you can give me some advice on this.

Best regards,
Tu Le