VMD-L Mailing List

From: Wenhao Liu (mdsimulate_at_gmail.com)
Date: Wed Apr 17 2013 - 12:46:20 CDT

Chris,
I read the CGenFF paper and I think it didn't discuss much about carbonyl
group. So you mean the reason why ffTK generate three water-molecule
complexes for oxygen in carbonyl group is to let MM values approach QM
values, right? So when I optimize the charges in ffTK for the moelcule
contain carbonyl group, I should use all these three(120a, 120b, 180)
gaussian log files for carbonyl oxygen in my QM target data, right?

Wenhao

On Wed, Apr 17, 2013 at 1:26 PM, Mayne, Christopher G
<cmayne2_at_illinois.edu>wrote:

> Carbonyls are a special case in ffTK. The optimal water positioning in
> QM is 120 degrees (where the electron density is located. In MM, the force
> field uses a point charge model that doesn't account for electronic
> structure, hence, the optimal water position is 180 degrees to reduce
> steric interaction with adjacent bound atoms. In this special case, ffTK
> generates input files for BOTH 120 and 180 degree positioning of waters, as
> per the suggestion made either on the CHARMM forums or in the original
> CGenFF paper (I don't remember where off the top of my head). This
> essentially hedges against errors due to discrepancies between QM and MM
> theories.
>
> Christopher Mayne
>
> PS Wenhao, we should keep this discussion on-list
>
> On Apr 17, 2013, at 12:18 PM, Wenhao Liu wrote:
>
> Chris,
> I see your point about charge optimizer. Thanks. So the plugin can
> generate more than one acceptor or donor bonding with water molecules for
> the atoms in my new molecule(like oxygen) if it can form more than one
> bond, right? I think this should be right since I've just tried and find
> that the plugin generated three different water bonding structures for the
> oxygen in Carboxyl group and that make sense.
>
> Wenhao
>
>
> On Wed, Apr 17, 2013 at 10:52 AM, Mayne, Christopher G <
> cmayne2_at_illinois.edu> wrote:
>
>> I don't think so. The optimizer judges the ability of a charge set to
>> reproduce the interaction, but the positioning of the water is
>> predetermined based on geometry, i.e., not a stochastic calculation. The
>> best time to modify your weights is when you want to bias the charge sets
>> towards getting a particular interaction correct (relative to qm).
>>
>>
>>
>> On Apr 17, 2013, at 9:18 AM, "Wenhao Liu" <mdsimulate_at_gmail.com> wrote:
>>
>> Chris,
>> So you mean I can set the weight like to 2 when I deal with oxygen-water
>> bonding in the condition that oxygen in my new molecule can form two
>> hydrogen bonds with water? Thank you!
>>
>> Wenhao
>>
>> 在 2013年4月17日星期三，Mayne, Christopher G 写道：
>>
>>> It is not required due to the symmetry of water--there is no extra
>>> information to be gained by flipping the identities of the hydrogens. ffTK
>>> handles the positioning of the water automatically.
>>>
>>> Regards,
>>> Christopher Mayne
>>>
>>>
>>> On Apr 17, 2013, at 1:53 AM, Wenhao Liu wrote:
>>>
>>> > Hello vmd people,
>>> > I was just wondering is it required to set up more than 1 hydrogen
>>> bonding for Acceptor (like the oxygen that can bonding with 2 hydrogen of
>>> the water) when I need to do the water interaction Gaussian calculation in
>>> charge optimization step? But I can only have 1 possible conformation to
>>> put water molecule bonding with oxygen in Acceptor indices, the other
>>> possible hydrogen boding between oxygen and hydrogen of water should be in
>>> different orientation, right? Or I can just set the weight of this
>>> calculation to 2 when I do the charge optimization? Thanks in advance.
>>> >
>>> > Wenhao
>>>
>>>
>
>