AMBER Archive (2008)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Sat Sep 27 2008 - 08:56:22 CDT

it looks like there might be something called OXT in the input pdb.
this is only valid for terminal residues. it doesn't look like LYS240
is terminal- make sure you have TER lines between your monomers.
is the residues named CL an ion? check the pdb to see what it is, you
might need to change the name.

On Sat, Sep 27, 2008 at 9:46 AM, Francesco Pietra <chiendarret_at_gmail.com> wrote:
> Hi:
> I have a problematic pdb file for leap (or for me!). It is for a
> multimer created with Modeller and contains chloride ions ligands.
>
> Before MD with Amber I attempted docking of both polypeptides (DOT2)
> and small molecules (DOCK6.2). The first ones successful, the second
> ones unsuccessful at the Amber score stage. Command "prepare_amber.pl"
> did not recognize the CL residue (which is a problem that I'll discuss
> at dock-fans)
>
> Therefore, I made recourse to leap (Amber10, Amber tools 1.0), loading
> "leaprc.ff99SB" and "leaprc.gaff" only. This resulted in a couple of
> errors for each chain for failure to deal with "atom named OXT" and
> "residue CL".
>
> From leap.log for the first chain:
>
> Unknown residue: CL number: 420 type: Terminal/last
> ..relaxing end constraints to try for a dbase match
> -no luck
>
> Created a new atom named: OXT within residue: .R<LYS 420>
> Creating new UNIT for residue: CL sequence: 421
> One sided connection. Residue: missing connect0 atom.
> Creating a new atom named: CL within residue: .R<CL 421>
>
> Similarly for the other chains. Finally
>
> WARNING: The unperturbed charge of the unit: -47.000000 is not zero.
> FATAL: Atom .R<LYS 420>.A<OXT 23> does not have a type.
>
> Similarly for the other chains.
>
> Does that suggest that I must load some other files into leap besides
> ff99SB and gaff, or other changes are suggested by the OXT issue?
>
> Thanks
>
> francesco pietra
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