[gmx-users] pdb2gmx fatal error

[Justin Lemkul]

On 11/7/18 1:05 PM, Ali Khodayari wrote:
> Dear gmx users,
>
>   
>
> I am trying to simulate a cellobiose, using GROMOS53a6CARBO. The atom names
> were modified according to the rtp file of the force field. Yet, I get the
> following error while I perform pdb2gmx command:
>
>   
>
> Fatal error:
>
> Residue 4 named GLC of a molecule in the input file was mapped to an entry
> in the topology database, but the atom C6 used in that entry is not found in
> the input file. Perhaps your atom and/or residue naming needs to be fixed."
>
>   
>
> I also tried to delete the hydrogens in the pdb file but the error changed
> to the following:
>
>   
>
> Fatal error:
>
> Residue 876814369 named GLC of a molecule in the input file was mapped to an
> entry in the topology database, but the atom C3 used in an interaction of
> type improper in that entry is not found in the input file. Perhaps your
> atom and/or residue naming needs to be fixed.
>
>   
>
> Ignoring the hydrogens through -ignh will give the first error as well.
> Then I added the GLC residue to the residuetypes.dat and the error changed
> to:

Your problem is not related to hydrogens. pdb2gmx is complaining about 
carbon nomenclature.

http://www.gromacs.org/Documentation/Errors#Atom_X_in_residue_YYY_not_found_in_rtp_entry

>   
>
> Fatal error:
>
> atom N not found in buiding block 1GLC while combining tdb and rtp
>
>   

This error comes from letting pdb2gmx apply default protein terminal 
patches. For a carbohydrate, you probably should have definitions for 
properly constructed reducing and non-reducing ends (e.g. different from 
internal residues) and apply no terminal patching.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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jalemkul at vt.edu | (540) 231-3129
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