From: rodolfo gonzalez (rodogonza234_at_gmail.com)
Date: Tue Oct 22 2013 - 05:26:31 CDT

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
> 3155Ė3168), 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 donít 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
>>
>>
>
>
>
>