Hi Jason,
Thanks for pointing me in the right direction. I have one follow up question. In the code snippet here below the C1, C2, and C3 atomtypes, am I correct if I think these are either united-atoms (e.g. CH3) or belonging to NA (e.g. C1')?
if molecule.elements[i] == 'C':
if parm.parm_data['AMBER_ATOM_TYPE'][i][:2] in ['C1', 'C2', 'C3']:
parm.parm_data['RADII'][i] = 2.2
else:
parm.parm_data['RADII'][i] = 1.7
Best,
Jesper
On May 20, 2012, at 3:59 PM, Jason Swails wrote:
> In parmed you can look in Ambertools/src/parmed/ParmedTools/changeradii.py (i think, i dont have the source handy to confirm) for the rules. Hopefully it is easy enough to glean from the source code there (it is trickier in the leap sources, IMO).
>
> HTH,
> Jason
>
> --
> Jason Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
>
> On May 17, 2012, at 8:26 AM, Jesper Sørensen <jesorensen.ucsd.edu> wrote:
>
>> Hi Jason,
>>
>> This is an old posting, but could you point me to the place where these atom radii are stored in the source code, either for Leap or ParmEd?
>>
>> I want to try and make a radii/charges file for pdb2pqr, to generate e.g. bondi radii and amber charges, to be used for PB calculations with APBS or DELPHI.
>>
>> Thanks,
>> Jesper
>>
>>
>>
>> On May 2, 2012, at 1:07 PM, Jason Swails wrote:
>>
>>> What Hai was saying is that "set default pbradii mbondi3" is identical to
>>> "set default pbradii mbondi2" for all atoms except 3 atom types [HH(Arg)
>>> and OE(Glu), OD(Asp)].
>>>
>>> Also, the atom radii are NOT stored in the force field files (e.g.,
>>> gaff.dat, parm99.dat, etc.). They are stored in the LEaP (and ParmEd)
>>> source code. If you want to use the mbondi3 radii, you should load mbondi3
>>> at the beginning -- the ligand will be treated as though the radii set was
>>> mbondi2.
>>>
>>> HTH,
>>> Jason
>>>
>>> On Wed, May 2, 2012 at 11:05 AM, Jesper Sørensen <jesorensen.ucsd.edu>wrote:
>>>
>>>> Thank you Hai. But it is likely that the ligand radii are coming from the
>>>> GAFF parameters.
>>>>
>>>> I wonder if the correct procedure would probably be to "set default
>>>> PBradii mbondi3" before loading in the ligand - then only the protein radii
>>>> should change to mbondi3, without trying to alter the ligand radii as well,
>>>> which again mbondi3 was likely not parameterized for?
>>>>
>>>> Or will this also change the ligand radii?
>>>>
>>>> Best,
>>>> Jesper
>>>>
>>>>
>>>>>
>>>>> For the ligand, mbondi3 should be exactly the same as mbondi2 since only
>>>>> radii of HH(Arg) and OE(Glu), OD(Asp) atom type are changed in mbondi3
>>>> from
>>>>> mbondi2.
>>>>>
>>>>> Best
>>>>> NHAI
>>>>>
>>>>>
>>>>> On Apr 30, 2012, at 9:02 AM, Ray Luo, Ph.D. wrote:
>>>>>
>>>>>> Jesper,
>>>>>>
>>>>>> Just a comment on a specific point in your email ...
>>>>>>
>>>>>> If you set radiopt=1 and have ligand (GAFF atoms) in the system, PBSA
>>>>>> would drop a bomb and quit. I believe this is the designed behavior.
>>>>>> This is because we don't have a "rule" to define the generic atomic
>>>>>> types in organic molecules. As you can image, the rule would require
>>>>>> far more simulation data to summarize than that for the proteins/NAs.
>>>>>>
>>>>>> So I don't think the scenario in your email would occur.
>>>>>>
>>>>>> If you have ligand (GAFFs), the only radii you can use with PBSA right
>>>>>> now is those in the prmtop file and those can be read in by "radiopt =
>>>>>> 0".
>>>>>>
>>>>>> It's not easy to mix different radii set for proteins/NAs and ligand
>>>>>> unless you can somehow revise the radii section in the prmtop file.
>>>>>>
>>>>>> Ray
>>>>>>
>>>>>> On Mon, Apr 30, 2012 at 12:11 AM, Jesper Sørensen <jesorensen.ucsd.edu>
>>>> wrote:
>>>>>> ...
>>>>>>> I know (Ambertools 12, section 8.2.3) that PBSA if you use
>>>> (radiopt=1), will stick to the Antechamber/GAFF radii for the ligand (and
>>>> perhaps even the FF radii for the protein) if there are GAFF parameters
>>>> present in the prmtop file, instead of swithing to the Tan & Luo radii
>>>> (TYL06 radii). But perhaps this is only a requirement for the TYL06 radii
>>>> and not mbondi* radii? Can you clarify this a bit for me?
>>>>>>>
>>>>>>> Best,
>>>>>>> Jesper
>>>>>>>
>>>>>>>
>>>>>>
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>>>>>
>>>>
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>>>>
>>>
>>>
>>>
>>> --
>>> Jason M. Swails
>>> Quantum Theory Project,
>>> University of Florida
>>> Ph.D. Candidate
>>> 352-392-4032
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
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Received on Wed May 23 2012 - 15:30:02 PDT
