VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Wed Dec 22 2010 - 00:50:35 CST

To be more specific, autopsf recognizes the CT2 segment as
non-protein. Therefore, in the gui I edit:

-- the PHE segment 1-81, adding 82-86 in a single segment 1-86

--N terminal patch, from NTEr to CT2

--C terminal patch from CTER to CT2

-- delete the 82-86 segment

--Selection from 'everything' to 'protein'

The display now shows the entire PHE-CT2

I have tried other combinations in the gui but always ending in "
error: failed on end of segment". Either (very likely) my procedure is
incorrect or autopsf gets confused by CT2. I have considered related
problems on the VMD mail list.

thanks

francesco

---------- Forwarded message ----------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Tue, Dec 21, 2010 at 6:49 PM
Subject: vmd-l: autopsf error: failed on end of segment
To: vmd-l_at_ks.uiuc.edu

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