Hi Jason and others,
If you do specify:
> "set default pbradii mbondi3" in tleap
Similar to this example from the manual (Ambertools 12, section 10.2.1)
> A sample script file called, for instance, mmpbsa_leap.in, is shown below
>
> source leaprc.ff99SB
> loadAmberParams LIG.frcmod
> LIG = loadMol2 LIG.mol2
> receptor = loadPDB receptor.pdb
> complex = combine {receptor LIG}
> set default PBRadii mbondi2
>
> saveAmberParm LIG lig.top lig.crd
>
> saveAmberParm receptor rec.top rec.crd
>
> saveAmberParm complex com.top com.crd
>
> solvateOct complex TIP3PBOX 15.0
> saveAmberParm complex com_solvated.top com_solvated.crd
> quit
Don't you also alter the ligand radii? Were the mbondi* radii's developed for this or should you stick with the GAFF parameters for the ligand?
Again, this may just be a matter of "taste", but I figure it can't hurt asking.
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
On Apr 28, 2012, at 1:32 PM, Jason Swails wrote:
> There are two ways of specifying the mbondi3 radii in AmberTools 12. You
> can use "set default pbradii mbondi3" in tleap (as NHAI suggested), or you
> can use ParmEd (parmed.py or xparmed.py) if you already have a topology
> file and just change the radii to mbondi3.
>
> HTH,
> Jason
>
> On Sat, Apr 28, 2012 at 2:07 PM, Mike NG <nhai.qn.gmail.com> wrote:
>
>> You can specify 'mbondi3' in tleap of amber12.
>>
>> Best
>> NHAI
>>
>> On Tue, Sep 6, 2011 at 1:56 PM, Peter Varnai <P.Varnai.sussex.ac.uk>
>> wrote:
>>
>>> Dear All,
>>>
>>> This is to inquire whether there has been any update regarding the
>> mbondi3
>>> parameters for protein simulations with igb=8.
>>>
>>> The amber11 manual states (p. 57) that the mbondi2 radii are fine to use
>>> with igb=8 which Carlos mentioned is the case indeed on 27 April but some
>>> new modifications are available to improve those results for salt
>> bridges.
>>> The manual also details new scaling and atom-specific parameters which
>> all
>>> seems to have been implemented in mdread.f (apparently these can be
>> changed
>>> in the mdin file).
>>>
>>> I would be happy to update the protein atom radii in the prmtop file to
>>> the most recent mbondi3 values: (i) has the paper been published that
>> gives
>>> those values? (ii) Jason's python script may be made available that
>>> corrects for those? (iii) is there a leap fix available?
>>>
>>> Many thanks,
>>> Peter
>>> _______________________________________________
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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
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>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Mon Apr 30 2012 - 00:30:03 PDT
