problem with PSFGEN: the O3A atom cannot be recognized

From: Shirley Li (li19104_at_yahoo.com)
Date: Tue Oct 11 2005 - 12:52:49 CDT

Thanks a lot for the quick response. It helps to run
these commands in tkcon window. Now I got an error
message as follows:

ERROR: Missing atoms for bond O3A(0) PB(0)
ERROR: Missing atoms for bond PA(0) O3A(0)

Actually, psfgen couldn't recognize the O3A atom in
GTP in my .pdb file. I have the top/param in the
topology and parameter files. I also have the coord.
for this O3A atom in my .GTP file, with the atom order
either the same or different from the order in the
topology file causing the same error message.

What could be the problem?

Thanks a lot for your help in advance.

Shirley

--- JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:

> All I can see offhand is a typo towards the end,
> where you use GTPP
> once for the segment and GTPA in the next line.
>
> You can also run these commands individually in the
> tkcon window; that
> might help you find out where something is going
> wrong.
>
> On Oct 10, 2005, at 6:15 PM, Shirley Li wrote:
>
> > Dear NAMD experts,
> >
> > I have two questions about psfgen as follows:
> >
> > 1) The protein has two chains, and it contains
> GTP. I
> > was using psfgen by typing:
> > "vmd -dispdev text -e psfgen". While I got
> warning
> > messages that it failed to set coord. for any
> atom.
> > As the result, both the output file "out.pdb" and
> > "out.psf" are empty. The script is attached
> below,
> > which is the copy of the one in NAMD website with
> some
> > changes. Could someone please help me out?
> >
> > 2) Besides, since the terminal residues on both
> chains
> > need to be terminated with ACE/CT3 residues, I
> wonder
> > if it works in the way I set in the psfgen script.
> >
> > ---------------- psfgen ----------
> > package require psfgen
> > topology ./top_all27_prot_na_gtp_gdp.inp
> > #pdbalias residue HIS HSE
> > pdbalias atom ILE CD1 CD
> > segment ALPH {
> > pdb protein-ALPH.pdb
> > first ACE
> > last CT3
> > }
> > coordpdb protein-ALPH.pdb ALPH
> > segment BETA {
> > pdb protein-BETA.pdb
> > first ACE
> > last CT3
> > }
> > coordpdb protein-BETA.pdb BETA
> > segment GTPP { pdb protein-GTP.pdb }
> > coordpdb protein-GTP.pdb GTPA
> > guesscoord
> > writepsf out.psf
> > writepdb out.pdb
> > exit
> >
> > ----------------------
> >
> >
> >
> > __________________________________
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>

                
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