AMBER Archive (2008)

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

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sat Sep 27 2008 - 10:36:47 CDT

I reply here also to carlos, with thanks.

The OXT issue was resolved by placing an additional TER line (I forgot
the HETATM is not recognized by Amber as not needing TER, so that
there was a TER line only after the CL line, before next chain. That
is, CL was in the same first chain, and so on)

The interface between the first two chains reads now:

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

However the CL/Cl- issue was not resolved. Apparently, Cl- is not
recognized as a residue:

WARNING: The unperturbed charge of the unit: -50.000000 is not zero.
FATAL: Atom .R<Cl 421>.A<Cl- 1> does not have a type.

Should I try "Cl" as residue and "Cl-" as atom name?

I'll take care of the (very delicate problem) total charge only when
present FATALS are resolved.

Thanks
francesco

On Sat, Sep 27, 2008 at 4:12 PM, David A. Case <case_at_biomaps.rutgers.edu> wrote:
> On Sat, Sep 27, 2008, Francesco Pietra wrote:
>
>> I have a problematic pdb file for leap (or for me!). It is for a
>> multimer created with Modeller and contains chloride ions ligands.
>>
>> Created a new atom named: OXT within residue: .R<LYS 420>
>
> Do you have a TER card between residue 420 and 421? This is needed so
> that Amber knows that Lys 240 is at the end of the chain, and hence
> should have an OXT atom.
>
>> Creating new UNIT for residue: CL sequence: 421
>
> The Amber residue name for a chloride ion is "Cl-", and the
> corresponding atom name is "Cl-" as well. You will probably need to
> adjust your pdb input file.
>
> [Do people know if "CL" is really a pdb/rcsb supported standard? If so,
> we should probably either update ions08.lib, or add appropriate
> translation lines in the standard leaprc files.]
>
> ...dac
>
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