Fwd: [gmx-users] Fatal error:Atom S in residue TYR 2 not found

[Tsjerk Wassenaar]

Hi Winter,

Please keep discussions on the list, so that they will be recorded for
future reference (still optimistically assuming lots of people search
the archives before posting messages).

The problem will be in your .pdb file. Somehow, pdb2gmx finds a
sulphur which it 'thinks' belongs to a tyrosine. Have you checked the
residue indicated? Are there multiple residues with the same number?
Where is the 'S' and where does it belong to? Try to find the answers
to these (and other) questions yourself. If you've checked the .pdb
file thoroughly and know it's 'normal', i.e. should process without
problems, but find that it doesn't, please report back with the .pdb
file as attachment (sending a single structure). Do consider that
pdb2gmx is one of the commonly used (though most obscure) programs and
doesn't just give such errors for the fun of it.

Cheers,

Tsjerk


---------- Forwarded message ----------
From: kong.winter <kong.winter at gmail.com>
Date: May 8, 2007 8:35 AM
Subject: Re: [gmx-users] Fatal error:Atom S in residue TYR 2 not found
To: tsjerkw <tsjerkw at gmail.com>


Tsjerk,
Hi,
Thank you for your reply.
I added the missing atoms to my PDB file by the package "Swisspdb",
and solved the WARNING (WARNING: atom CD not found in residue 72 while
adding improper )

But the fatal error hasn't been solved, i.e "Atom S in residue TYR 2
not found in rtp entry with 18 atoms while sorting atoms". Yes,
there's no S in TYR. I don't what's the reason.

Thank you again.

Winter,



Message: 6
Date: Tue, 8 May 2007 06:52:47 +0200
From: "Tsjerk Wassenaar" <tsjerkw at gmail.com>
Subject: Re: [gmx-users] Fatal error:Atom S in residue TYR 2 not found
       in rtp       entry with 18 atoms
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Message-ID:
       <8ff898150705072152u4356e6d6k21a2e6181b20c346 at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi Winter,

> I'm a beginner to GMX,
> when I use the following command:
> "pdb2gmx -f 1G1S.pdb -p gr.top -o gr.gro -missing"

Don't use '-missing'. Since you're a beginner you're not allowed to
(unless you get a permit for it from one of the developers).

> "WARNING: atom CD not found in residue 72 while adding improper

This is the result of using '-missing'.

> Fatal error:
> Atom S in residue TYR 2 not found in rtp entry with 18 atoms
>              while sorting atoms"
>
> How to solve this fatal error?

Well, as I recall, but I may need to check my biochemistry books here,
there's no S in tyrosine. Is this a modified residue, or is there just
something _else_ wrong with your starting structure? Note that I say
something else, since you clearly also have missing atoms, which you
need to fix. Go work on the starting structure!

Best,

Tsjerk



-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623