AMBER Archive (2008)

Subject: Re: AMBER: Leap atoms CL and OXT do not have a type

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Sat Sep 27 2008 - 11:29:23 CDT

On Sat, Sep 27, 2008, Francesco Pietra wrote:
>
> ATOM 3422 OXT LYS A 420 153.130 56.796 73.930 1.00 97.96 1SG3423
> TER
> HETATM 3423 Cl- Cl-A 421 80.566 52.944 60.971 1.00 6.32 1SG3425
> TER
> ATOM 3424 N LEU B 1 148.531 90.864 79.387 1.00 63.95 2SG3426

Looks to me like you have the residue name for the Cl- residue in the
wrong columns in your pdb file. Residue names need to be in columns
18-20 of each atom or hetatm record.

> FATAL: Atom .R<Cl 421>.A<Cl- 1> does not have a type.

This should be your clue: LEaP thinks the residue name is "Cl", not
"Cl-". Also, just visually note that the residue name for the ion does
not match up with the residue names before and after for the amino
acids.

...dac

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