Re: psfgen operation for the C terminal of HSE

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Mon Mar 27 2006 - 08:43:22 CST

Dear Shulin,
these warnings are fairly common; they just come because psfgen has to
guess the coordinates for the C terminus. You should just look at your
output psf/pdb and make sure it looks reasonable.
Peter

Shulin Zhuang wrote:

> Dear All,
>
> When I use psfgen program to make the parameter file for my protein,
> it tell me that"Warning: failed to set coordinate for atom O
> HIS:118 A".
> In the C terminal is the residue HIS which is aliased to be HSE. The
> last two residue in the segments of my protein are HIS.
>
> My command is as follows:
> topology top_all22_prot.inp
> pdbalias residue HIS HSE
> pdbalias atom ILE CD1 CD
>
> segment A {
> pdb chainA.pdb
> }
>
> when I type:
> coordpdb chainA.pdb A
>
> the message arise:
> reading coordinates from pdb file gdo_frag0.pdb for segment A
> Warning: failed to set coordinate for atom O HIS:118 A
>
> when I further type:
> guesscoord
> it tells me that:
> Warning: poorly guessed coordinate for atom OT1 HSE:118 A
> Warning: poorly guessed coordinate for atom OT2 HSE:118 A
>
> Are thes warning normal?
>
> Should I use
> segment A {
> pdb chainA.pdb
> last none
> }
>
>
> --
> Shulin Zhuang
> Chemistry Department
> Zhejiang University PRC
> shulin.zhuang_at_gmail.com <mailto:shulin.zhuang_at_gmail.com>

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