I will try out your suggestions.
Thank You
Martina
On Sun, Jun 12, 2016 at 6:48 AM, David A Case <david.case.rutgers.edu>
wrote:
> On Sat, Jun 11, 2016, Martina Devi wrote:
>
> > The residue is a non-standard base which contain -COO ionised substituent
> > attached to the base. I added Hydrogen to the O of -COO group through
> > xleap graphical interface.then I tried to save and quit but it shows the
> > presence of errors.Then I gave the atom names and atom types in the table
> > and tried to save and quit, it shows error.
>
> I'm sorry, but the above description is not very helpful: it doesn't give
> nearly enough information about what you did, and (more importantly) what
> the errors were. Saying something like "it shows the presence of errors"
> does not allow anyone else to help you: what was the error (exactly)?
>
> Try working first on something that doesn't involve a non-standard
> residue. For example, load a protein force field, edit the ASP residue,
> and try to add a hydrogen atom to the side chain carboxylate. See if you
> can
> get this work. I know it is hard to describe mouse actions in an email,
> but
> (if you have problems) try hard to explain exactly what steps you took.
>
> >
> > How do I solve the above errors. Or is there other method to add
> Hydrogen.
>
> There are many other programs that allow you to graphically build
> molecules,
> and many of them have interfaces that may be more intutivie that xleap.
> If you save the coordinates in PDB format, you can use that as input to
> antechamber (for example) to create a UNIT for your non-standard base.
>
> ....good luck....dac
>
>
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Received on Tue Jun 14 2016 - 00:30:02 PDT
