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 - 13:21:19 CDT

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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