[gmx-users] error in pdb2gmx step

[Annie Albin]

Well thank you.Yes I did find a region in which chain identifier 'A' was
repeating, this corresponded to the HETATM CO, so i tried removing the chain
identifier in one case and in another one I tried shifting it to the
correspoding chain, but in both cases i got the following error
"Fatal error:
Residue 'CO' not found in residue topology database".
Will be glad to hear any suggestions.
Is there any other way in GROMACS to handle proteins with metal ions in it?

Thank You,
Annie Albin.



On 3/31/06, MGiò <magiofer at gmail.com> wrote:
>
> Hi!
> it seems that pdb2gmx has detected an interruption in your chain A
> numbering, are you sure that there are none? or else are you sure that
> you're not using the same chain id for more than one chain? for example for
> two different monomers?
> hope it helps,
> MG
>
> On 3/31/06, Annie Albin < anniealbin at gmail.com> wrote:
>
> > Dear all,
>
>  I faced a problem in the  pdb2gmx step as i got this following error
> message,
> "Fatal error:
> Chain identifier 'A' was used in two non-sequential blocks (residue 908,
> atom 7013)"
>
> As I'm pretty new to this field. I'm finding it difficult to troubleshoot.
> Any suggestions would be of great help.
> Thank you,
> Annie Albin.
>
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