[gmx-users] Re: [gmx-developers] Off-by-one error in pbd2gmx

[Anton Feenstra]

Berk Hess wrote:
> 
> >
> >WARNING: atom CD is missing in residue LEU 26 in the pdb file
> >WARNING: atom CE is missing in residue LEU 26 in the pdb file
> >WARNING: atom NZ is missing in residue LEU 26 in the pdb file
> >WARNING: atom CE is missing in residue TYR 42 in the pdb file
> >WARNING: atom NZ is missing in residue TYR 42 in the pdb file
> >WARNING: atom OD1 is missing in residue PHE 50 in the pdb file
> >WARNING: atom OD2 is missing in residue PHE 50 in the pdb file
> >WARNING: atom CG is missing in residue ASN 99 in the pdb file
> >WARNING: atom OD1 is missing in residue ASN 99 in the pdb file
> >WARNING: atom ND2 is missing in residue ASN 99 in the pdb file
>
[..snip..]
> 
> Another question is if this should be a warning or an error message.
> In this case a topology will be generated where some atoms are not
> present. My opinion is that pdb2gmx should generate a fatal error
> after printing all the missing atoms.

Couldn't we make a directive like '[ faulty_topology ]' that pdb2gmx
adds to the .top file in this case and which would cause grompp to 
refuse to generate a .tpr file? That way, if someone wants to do some 
strange things for some reason, that would be possible by manually 
removing the directive from the .top file.

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
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