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 Sat Jun 11 2016 - 18:30:02 PDT
