VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Dec 21 2010 - 11:49:14 CST

Hello:
With VMR 1.8.7 I am trying to generate psf for a protein ending with
amidated phenylalanine, using validated top_all27_prot_na.rtf. I tried
also 'source autopsf.tcl', using a recent script, before autopsf.  It
always crashes with error: failed on end segment.

The pdf file ends with (here I tried separately chain D, renumbering
atoms) using the method for amber:

ATOM     80  HE2 PHE D   4     -31.197  22.536   3.559  1.00  0.00      4SG  H
ATOM     81  HZ  PHE D   4     -30.544  24.713   4.555  1.00  0.00      4SG  H
ATOM     82  C   CT2 D   5     -32.820  18.877   8.926  1.00  0.00      4SG  C
ATOM     83  O   CT2 D   5     -34.065  18.451   9.222  1.00  0.00      4SG  O
ATOM     84  NT  CT2 D   5     -31.788  18.180   9.397  1.00  0.00      4SG  N
ATOM     85  HT2 CT2 D   5     -30.844  18.477   9.196  1.00  0.00      4SG  H
ATOM     86  HT1 CT2 D   5     -31.949  17.354   9.956  1.00  0.00      4SG  H

Is that correct?

Thanks for help

francesco pietra