VMD-L Mailing List
From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Wed Oct 19 2005 - 18:15:26 CDT
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- In reply to: phoenix: "Warining when generating psf file"
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It's just an atom name mismatch between your pdb file and the topology
file. Hydrogen coordinates can be easily generated automatically, so it's
probably nothing to worry about.
-Jim
On Sun, 16 Oct 2005, phoenix wrote:
> Hi all,
> when I generating psf file by the psfgen pluging,It give me some Warnings
> like below.Is there something unusual???
> reading coordinates from pdb file 1f0d_1.pdb for segment FDAA
> Warning: failed to set coordinate for atom 1H LYS:1 FDAA
> Warning: failed to set element for atom 1H LYS:1 FDAA
> Warning: failed to set coordinate for atom 2H LYS:1 FDAA
> Warning: failed to set element for atom 2H LYS:1 FDAA
> Warning: failed to set coordinate for atom 3H LYS:1 FDAA
> Warning: failed to set element for atom 3H LYS:1 FDAA
> Warning: failed to set coordinate for atom 1HB LYS:1 FDAA
> Warning: failed to set element for atom 1HB LYS:1 FDAA
> Warning: failed to set coordinate for atom 2HB LYS:1 FDAA
> Warning: failed to set element for atom 2HB LYS:1 FDAA
> Warning: failed to set coordinate for atom 1HG LYS:1 FDAA
>
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