maybe check your leap log and see if it is loading ion libs or not?
On Sat, Sep 27, 2008 at 11:36 AM, Francesco Pietra
<chiendarret.gmail.com> wrote:
> 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.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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Received on Sun Sep 28 2008 - 05:11:07 PDT
