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