[gmx-users] error in pdb2gmx step

[Annie Albin]

True. I checked the files and found that CO was not described in any of them
and I did take care of the replacement ot A with a blank.
 Well in this case do I have any alternatives?
Like other compatible force fields or modification of the existing one.

Annie Albin.


On 3/31/06, MGiò <magiofer at gmail.com> wrote:
>
> That means that the CO ion type is not described by the forcefield you are
> using, check the .rtp file of your force field or the ions.itp file in the
> gromacs/top directory. anyhow be careful not to make any confusion between
> the chain identifier, which is a 1 character id, and the residue name. Are
> you sure you're not shifting the columns of your pdb when deleting the chain
> identifier (chain A shoud be replaced by a blank)?
>
>
> MG
>
> On 3/31/06, Annie Albin <anniealbin at gmail.com> wrote:
> >
> > 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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