[gmx-users] Fatal error: Atom O in residue COC 1 not

[David van der Spoel]

On Wed, 2004-11-24 at 15:38 -0800, Yunfeng Hu wrote:
> I do not know if anything else needs to be done. Here is the error 
> message after pdb2gmx -ter or -ighn
> ...
> Looking whether force field file ffG43a1.rtp exists
> Opening library file ffG43a1.rtp
> Opening library file aminoacids.dat
> Reading 1.pdb...
> Read 22 atoms
> Opening library file /usr/local/gromacs/share/top/xlateat.dat
> 23 out of 23 lines of xlateat.dat converted succesfully
> Analyzing pdb file
> There are 1 chains and 0 blocks of water and 1 residues with 22 atoms
> 
>    chain  #res #atoms
>    1 'X'     1     22
> 
> All occupancy fields zero. This is probably not an X-Ray structure
> Opening library file /usr/local/gromacs/share/top/ffG43a1.atp
> Atomtype 50
> Reading residue database... (ffG43a1)
> Opening library file ffG43a1.rtp
> Residue 97
> Sorting it all out...
> Opening library file ffG43a1.hdb
> Opening library file /usr/local/gromacs/share/top/ffG43a1-n.tdb
> Opening library file /usr/local/gromacs/share/top/ffG43a1-c.tdb
> Processing chain 1 'X' (22 atoms, 1 residues)
> Opening library file /usr/local/gromacs/share/top/specbond.dat
> 5 out of 5 lines of specbond.dat converted succesfully
> There are 0 donors and 1 acceptors
> There are 0 hydrogen bonds
> Fatal error: Atom O in residue COC 1 not found in rtp entry with 22 
> atoms
>               while sorting atoms
Could it be that you have typed 0 (zero) instead of O (oxygen)?

> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++