VMD-L Mailing List

From: rodolfo gonzalez (rodogonza234_at_gmail.com)
Date: Tue Oct 22 2013 - 09:33:02 CDT

Hi Christopher,
Really clear explanation, thanks a lot!

Kind Regards

On 22 October 2013 14:00, Mayne, Christopher G <cmayne2_at_illinois.edu> wrote:

> Rodolfo,
>
> The "acceptable" range for the final objective function (assuming
> convergence) will be optimization specific--meaning it will depend on the
> compound, target data, and weighting. Generally speaking, lower is better;
> however, one should also take the relative contributions of the summed
> terms (energy, distance, & dipole), as well as the individual interactions,
> into account when considering the quality of the fit. The target values
> for specific interactions, as coded into the objective function, are 0.2
> kcal/mol and 0.1A for interaction energies and minimum distances,
> respectively. In practice, about 2x these values are generally acceptable,
> depending on the nature of the interaction (i.e., how well the FF can
> represent the interaction).
>
> It's also important to know that the objective function is not
> normalized for the number of charges being optimized nor the amount of
> target data included in the fit. For large optimizations (many charges,
> lots of target data) this generally leads to larger final objective values,
> even for reasonable overall charges. For this, and many other important
> reasons, we suggest using a fragmentation approach where possible.
>
> Regards,
> Christopher Mayne
>
> On Oct 22, 2013, at 5:26 AM, rodolfo gonzalez wrote:
>
> Hi,
> Thanks a lot for all your valuable comments, they've been really helpful.
> I'll take a look for sure to the method used by paramchem and check on the
> usage of COLP. In any case now I think I have a clearer idea about how to
> proceed when facing charge parametrisation for a new compound.
> Christopher, I mentioned chlorobenzene just as an example but thanks
> anyway for your comments about it in CGenFF and about the intricacies of
> halogens in classical ff.
> One last question, about COLP, what is an acceptable range of values for
> the objective function convergence? Looking at the function it should be
> close to zero but that's in the ideal case of being able to precisely match
> the QM data, which I guess in real cases won't be possible, and also it
> will depend on the number of water-target interactions. I apologise if I
> missed a previous post about this issue, I couldn't find it.
>
> Many thanks for all your replies,
> Kind Regards.
>
>
>
> On 22 October 2013 00:20, Mayne, Christopher G <cmayne2_at_illinois.edu>wrote:
>
>> Rodolfo,
>>
>> To add to what Josh said, it might also be worthwhile to familiarize
>> yourself with the method ParamChem uses to compute partial atomic
>> charges (Vannomeslaeghe et al J. Chem. Inf. Model., 2012, 52 (12), pp
>> 3155–3168), to gain a better understanding of both the origin of the
>> charge calculation and the associated penalty score. We strongly encourage
>> users to validate these parameters using ffTK by taking advantage of the
>> utilities such as COLP. The ffTK documentation website contains a great
>> deal of information, including screencasts that demonstrate the use of
>> these tools.
>>
>> If you are explicitly interested in chlorobenzene, you should take a
>> look at the CGenFF parameter set which includes chlorobenzene
>> (residue=CHLB). It's also worth mentioning that parameterizing halogens
>> using a classical force field model (e.g., CHARMM, CGenFF) is quite
>> difficult due to electronic complexities.
>>
>> Regards,
>> Christopher Mayne
>>
>>
>>
>> On Oct 21, 2013, at 2:50 PM, Josh Vermaas wrote:
>>
>> Hi Rodolfo,
>>
>> It depends on what your aims are. If you want a transferrable set of
>> chlorobenzene parameters, that probably isn't a bad starting point for
>> simulations, and will yield parameters that are "close enough" with minimal
>> effort. If you were trying to get the most accurate parameter set possible
>> for chlorobenzene because the electron withdrawl by the chlorine is
>> something you believe is important to your work, it might be worth looking
>> at them again. It never hurts to check and see how good/bad the values
>> returned by paramchem are. I'd let FFTK set up all the water interactions
>> and just check with COLP if you are happy with the convergence overall with
>> the paramchem starting point (The water interactions are the cheapest
>> calculation in the grand scheme of things). If not, you may consider
>> letting the charges migrate from that starting point, as while paramchem's
>> algorithms get the general trends right, you can usually improve the
>> parameters if you spend a bit of time optimizing the charges.
>>
>> -Josh Vermaas
>>
>> On 10/21/2013 10:43 AM, rodolfo gonzalez wrote:
>>
>> Ok, for example if I wanted to parametrize a chlorobenzene and lets
>> assume that the paramchem penalties on all the atoms is below 10 except for
>> the Chlorine atom and the Carbon next to it. Then I would think that except
>> for these two atoms, the rest are similar to the corresponding ones in
>> benzene, and I would be tempted to keep the charges proposed by paramchem
>> for those atoms while trying to parametrize only the ones with high
>> penalty. Does it make any sense?
>>
>> Thanks
>>
>>
>> On 21 October 2013 13:59, Norman Geist <norman.geist_at_uni-greifswald.de>wrote:
>>
>>> What do you define as similar atoms?
>>>
>>>
>>> Norman Geist.
>>>
>>>
>>> *Von:* owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] *Im
>>> Auftrag von *rodolfo gonzalez
>>>
>>> *Gesendet:* Montag, 21. Oktober 2013 08:58
>>> *An:* Norman Geist
>>> *Cc:* Namd Mailing List; vmd-l_at_ks.uiuc.edu
>>> *Betreff:* Re: vmd-l: fftk-charges
>>>
>>>
>>> Hi,
>>>
>>> Thanks a lot for your answer. I understand the point about the
>>> importance of the specific environment on the atomic charges of each
>>> molecule. However, I thought that for transferability reasons and for
>>> keeping consistency with the rest of the compounds in the CGenFF the
>>> charges of similar atoms should be kept the same. Isn't that the reason why
>>> the server paramchem provides penalties when looking for homologous
>>> parameters for a new compound?
>>>
>>> Thanks again for your reply, as I am new to this procedures, this kind
>>> of discussions are really helpful.
>>>
>>>
>>> On 21 October 2013 07:23, Norman Geist <norman.geist_at_uni-greifswald.de>
>>> wrote:
>>>
>>> Hi,
>>>
>>>
>>> I don’t know if this is different in the charmm ff, but usually the
>>> partial charges are specific for compounds, or better called residues and
>>> not for atom types. Therefore one would usually compute the partial charges
>>> for a new residue from scratch for the whole molecule. I might be wrong
>>> here, but the partial charges depend a lot or almost only on the chemical
>>> environment. Means taking the charges from different molecules having a
>>> different chemical environment , is IMHO wrong.
>>>
>>>
>>> Norman Geist.
>>>
>>>
>>> *Von:* owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] *Im
>>> Auftrag von *rodolfo gonzalez
>>> *Gesendet:* Sonntag, 20. Oktober 2013 17:01
>>> *An:* vmd-l_at_ks.uiuc.edu
>>> *Betreff:* vmd-l: fftk-charges
>>>
>>>
>>> Hi,
>>>
>>> I am trying to parametrize a compound for which most atomic partial
>>> charges are already available in the CGenFF except for a few atoms. My
>>> question is: do I need to run the QM water-compund calculations for all the
>>> H-bond donors or acceptors atoms in my molecule or only for those whose
>>> atomic charge need to be parametrized?
>>>
>>> Thanks,
>>>
>>> Regards
>>>
>>>
>>
>>
>>
>>
>
>