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 - 14:31:51 CDT

Could you please suggest key readings about the pKa calculations at
issue? The behavior of a system of this type is expected to change
with the protonation state. From what I wrote before, protonation of
ASP and GLU is probably inhomogeneous in the system

Thanks
francesco

On Sat, Sep 27, 2008 at 8:21 PM, Carlos Simmerling
<carlos.simmerling_at_gmail.com> wrote:
> Be careful in changing the vdw of the ion- read the papers where the
> ion set was developed first.
>
> as far as His protonation goes, unless you specifically do a
> calculation to determine pKa, His will be treated as HIE. You need to
> change the name to HIP if you want it protonate. none of the Amber
> setup programs look at environment and change protonation states
> without being told to do so.
>
> constant pH calculations are an active research area, so you're
> probably better off doing a pKa calculation and setting the
> appropriate constant protonation state.
>
>
> On Sat, Sep 27, 2008 at 2:11 PM, Francesco Pietra <chiendarret_at_gmail.com> wrote:
>> In answer also to Pr Case.
>>
>> On displacing Cl- to the wright columns for a residue, everything OK.
>> The prmtop and inpcrd files, as well as the pdb generated with ambpdb
>> open correctly in Chimera. Which means that ion libs were loaded. I
>> apologize for my lack of care.
>>
>> Now chloride is seen as a beautiful sphere, no more point-like as from
>> Modeller (where, I renounced to define the atom, though Modeller
>> conserved the X-ray diffr distances of the point from ligands). As the
>> conformation of the molecule is expected to depend from the vdw
>> assigned to Cl-, and that vdw is certainly not a constant for
>> different environments (Linus Pauling's story), in which file could
>> the vdw be changed? Certainly I should check now again the distances
>> from chloride and its ligands.
>>
>> One (for me) curious aspect of this protein is that neither HIS, nor
>> facing ASP-ASP or ASP-GLU are protonated, although they lie at (short)
>> H-bonding distances. Nothing was protonated, only HIS was changed to
>> HIE. Even Reduce did not protonate these residues. These are now
>> tricky problems, also because MD should probably at constant pH, while
>> the system will be in a membrane, and thus it would require constant
>> pH in explicit medium. I am prepared to wait, for this aspect, for
>> Amber# (#>13).
>>
>> Thanks a lot
>> francesco
>>
>> On Sat, Sep 27, 2008 at 7:07 PM, Carlos Simmerling
>> <carlos.simmerling_at_gmail.com> wrote:
>>> 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_at_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_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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