Re: missing atoms warnings for psfgen

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Thu Jan 22 2004 - 17:08:27 CST

Hi,

You errors that look like this:

no atom CD1 in residue ILE:140 of segment SEG7
Warning: failed to set coordinate for atom CD1 in residue ILE:140 of segment SEG7

are due to an atom name mismatch between the PDB and topology files. They
can be fixed by adding this alias:

alias atom ILE CD1 CD

See http://www.ks.uiuc.edu/Research/namd/2.5/ug/node21.html and scroll
down to the "pdbalias atom" command for the docs. Note that you're
running 2.5b1, and you should probably upgrade to 2.5. Also, the alias
command was renamed pdbalias (but the old one still works).

-Jim

On Mon, 19 Jan 2004, Frances Leung wrote:

> Hello,
>
> I'm working on a protein complex that has a large number of residues
> missing from the PDB file to begin with, when I was creating the psf
> structure file, I got a lot of warnings regarding missing atoms at the
> end of segment. Is this normal? Does the guesscoord command take care
> of adding back in all of the atoms? What should I do about the missing
> residues? The log file for generated the psf file is attached. The psf
> file was generated using the following script.
>
>
>
> topology parameters/top_all22_prot.inp
>
> alias residue HIS HSD
>
> # (2) Build protein segment and read coordinates
> segment seg0 {
> pdb myfile_frag0.pdb
> }
> coordpdb myfile_frag0.pdb seg0
>
> segment seg1 {
> pdb myfile_frag1.pdb
> }
> coordpdb myfile_frag1.pdb seg1
>
> segment seg2 {
> pdb myfile_frag2.pdb
> }
> coordpdb myfile_frag2.pdb seg2
>
> segment seg3 {
> pdb myfile_frag3.pdb
> }
> coordpdb myfile_frag3.pdb seg3
>
> segment seg4 {
> pdb myfile_frag4.pdb
> }
> coordpdb myfile_frag4.pdb seg4
>
> segment seg5 {
> pdb myfile_frag5.pdb
> }
> coordpdb myfile_frag5.pdb seg5
>
> segment seg6 {
> pdb myfile_frag6.pdb
> }
> coordpdb myfile_frag6.pdb seg6
>
> segment seg7 {
> pdb myfile_frag7.pdb
> }
> coordpdb myfile_frag7.pdb seg7
>
>
> # (3) Guess missing coordinates
> guesscoord
>
> # (4) Write structure and coordinate files
> writepsf output_psf/1i7x_psfgen_psf.psf
> writepdb output_psf/1i7x_psfgen_pdb.pdb
>
>
> Frances
>
>
>

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