AMBER Archive (2006)

Subject: Re: AMBER: LEaP not recognising Phosphate group in TYR

From: David A. Case (case_at_scripps.edu)
Date: Thu Dec 07 2006 - 11:06:17 CST

On Thu, Dec 07, 2006, bertrand russell wrote:

> I couldn't correct the FATAL errors for the added Phosphate group. I made
> changes is the input PDB file in reference to the contributed database
> entry. Eventhen, it is not recognising the atom types. I even tried adding
> the entry to the all_amino94.lib file which is in the leap's dat directory.
> But it is not recognising the Phosphorylated TYR residue.

Your description is not specific enough: you are saying logically what you
tried to do, but not what you actually did. What changes to the pdb file did
you make? What command did you you use to load the pTYR residue? What did
LEaP actually say?

....dac

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