Hi Junmei,
Just wondering how the Antechamber fix is going, and if you've learned
anything now about the scope of the problem.
Thanks,
Gabriel
On Wed, Feb 10, 2010 at 9:24 AM, Gabriel Rocklin
<gabriel.rocklin.ucsf.edu>wrote:
> Thanks Junmei. The parameters do more than maintain the planar
> conformation of the ring - they keep the ring substituents in plane with the
> rest of the ring. I'm not actually interested in imidazole and imidazolium
> themselves, but in their substituted versions, and binding free energies
> appear to change significantly when the ring substituents are allowed to
> bend when in protein complexes.
>
> Hope to hear from you by Monday.
>
> Gabriel
>
>
> On Wed, Feb 10, 2010 at 8:07 AM, Junmei Wang <
> Junmei.Wang.utsouthwestern.edu> wrote:
>
>> Dear Gabriel,
>> I will fix this no later than next Monday. Did you observe bizarre
>> behavior of gaff for imidazolium? It is true that the torsional angle
>> parameter of X-c2-na-X (2.5) is weaker than X-cc-na-X (6.8), but those
>> parameters are simply used to maintain the planar conformation of the ring.
>> The minimization or MD results of the two set of parameters should be very
>> similar anyway.
>>
>> Best
>>
>> Junmei
>>
>> >>> Gabriel Rocklin <gabriel.rocklin.ucsf.edu> 02/10/10 12:56 AM >>>
>> Dear Junmei,
>>
>> Do you have an estimate on how long that will take? I'd like to know
>> whether I should try to develop a workaround, or whether I can wait for
>> you.
>> Also, it would be good to know what the scope of the problem is as soon
>> as
>> you've identified it, even if you haven't yet designed a fix.
>>
>> Thanks,
>> Gabriel
>>
>>
>>
>> On Tue, Feb 9, 2010 at 9:07 PM, Junmei Wang
>> <Junmei.Wang.utsouthwestern.edu>wrote:
>>
>> > Dear Gabriel
>> > I got the same result as yours. It is not a correct antechamber
>> behavior. I
>> > will fix this bug as soon as possible. Thank you very much for reporting
>> > this problem
>> >
>> > I really appreciate your great help
>> >
>> > Junmei
>> >
>> >
>> > >>> Gabriel Rocklin <gabriel.rocklin.ucsf.edu> 02/09/10 1:33 AM >>>
>> > Dear Junmei and others,
>> >
>> > I am getting strange results when trying to parameterize some
>> heterocyclic
>> > cations using antechamber. Using a mol2 file for imidazole, when I do-
>> >
>> > antechamber -i imidazole.mol2 -o imidazole_out.prepi -fi mol2 -fo prepi
>> >
>> > I get a prep file for imidazole that has ring atom types cc, cd, and na.
>> > But when I do the same thing for imidazolium, I get atom types c2 and
>> na.
>> > Because GAFF c2 is not aromatic, the dihedral parameters about the ring
>> > become significantly weaker. The protonation should not affect the
>> > aromaticity like this, correct? I see the same thing
>> > for constitutively charged, n-substituted imidazoliums, as well as for
>> > thiazoles vs thiazoliums.
>> >
>> > Is this the correct antechamber / GAFF behavior? If so, why?
>> >
>> > I've attached the input and output files.
>> >
>> > Thanks,
>> > Gabriel
>> >
>> > Gabriel Rocklin
>> > UCSF Shoichet/Dill Labs
>> >
>> >
>>
>>
>
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Received on Mon Feb 15 2010 - 15:30:03 PST
