[gmx-users] pdb2gmx error

Justin A. Lemkul jalemkul at vt.edu
Mon Apr 9 22:05:03 CEST 2012

Bishwajit Das wrote:
> when i try to  pdb2gmx -f *.pdb -o *_processed.gro -water spce command 
> in my pdb file then i select  AMBER99SB-ILDN force field 
> (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010) this force field 
> but a error massage came.
> the massage is following:
> There are 0 donors and 0 acceptors
> There are 0 hydrogen bonds
> Identified residue GLU6 as a starting terminus.
> Identified residue GLU6 as a ending terminus.
> 8 out of 8 lines of specbond.dat converted successfully
> Start terminus GLU-6: NH3+
> End terminus GLU-6: COO-
> Checking for duplicate atoms....
> -------------------------------------------------------
> Program pdb2gmx, VERSION 4.5.4
> Source code file: /build/buildd/gromacs-4.5.4/src/kernel/pgutil.c, line: 88
> Fatal error:
> Atom CG not found in residue seq.nr <http://seq.nr>. 1 while adding atom
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------
>  then i repair my protein with what if server as instruction given in 
> gromacs documentation...then i again run the above process but still 
> showing me a error massage.The massage was His 450 chain is not 
> complete.How i overcome this problem..please give me a suggestion.

The exact error message, copied and pasted from your terminal along with any 
other relevant output, would be useful.  As it stands, the output you posted 
suggests that you have a single amino acid (since Glu-6 is both the start and 
end residue), but this is clearly not the case with the error at hand if 
something is wrong with His-450.

No matter the case, the general solution is that the atom naming must match that 
of the .rtp entry for the residue being processed.  If this is not true, either 
you are missing atoms or have a naming mismatch.  If the error arises due to a 
hydrogen atom, either use -ignh to ignore H atoms in the input and rebuild them, 
or fix the naming mismatch.

If you need further help, we need complete information.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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