VMD-L Mailing List

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Tue Dec 28 2010 - 17:03:41 CST

Is there any useful psfgen output preceeding that final error?

-Jim

On Wed, 22 Dec 2010, Francesco Pietra wrote:

> 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
>