AMBER Archive (2009)

Subject: Re: [AMBER] Atom type error

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Sun Apr 19 2009 - 12:41:11 CDT

On Sun, Apr 19, 2009, Vikas Sharma wrote:

> Thanks for the reply..but its the problem with the protein...since
> i prepared the protein in sybyl it has deprotonated the -COOh and
> protonated the -NH2.

This is the default for Amber as well. It could be that the residue
names for the N- and C-terminal residues are not Amber's (or the atom
names). Should be simple to just edit the PDB file to make things
match.

> >  Fatal: Atom .R<CXL 232>.A<C 1> doesnt have a type
> >  Fatal: Atom .R<CXL 232>.A<O2 2> doesnt have a type
> >  Fatal: Atom .R<CXL 232>.A<O1 3> doesnt have a type
> >  Fatal: Atom .R<AMN 233>.A<N 1> doesnt have a type

Amber doesn't know anything about residues named "CXL" or "AMN" -- you
will need to edit the PDB file to be more standard.

The usual rule of thumb applies here: you have to keep editing your PDB
file until LEaP stops complaining....

...dac

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