VMD-L Mailing List

From: Peterson J (peterson.jjjj_at_gmail.com)
Date: Tue May 21 2013 - 14:24:51 CDT

Thank you very much for your explanation. I will spend time looking into
the CGenFF to plan a scheme before I decide my QM run.

-Peterson

On Tue, May 21, 2013 at 1:05 PM, Mayne, Christopher G
<cmayne2_at_illinois.edu>wrote:

> Please take a closer look at the ffTK documentation website. It
> provides links to relevant materials that are essential for understanding
> parameterization. ffTK does not blackbox the process of parameterization;
> in fact, it does the exact opposite. Therefore, it is essential that you
> have a general understanding of the process to effectively use ffTK and
> generate reasonable parameters.
>
> If your compound of interest contains substructures that are highly
> analogous to existing fragments within the CGenFF standard distribution, we
> recommend that you retain those parameters, at least for a first pass
> parameterization. As I mentioned previously, if you are parameterizing
> from scratch, then the typing scheme is completely up to you.
>
> We intentionally choose pyrrolidine to use as our example molecules
> because:
> 1) the molecule exists in the standard CGenFF distribution. As I
> mentioned previously, by using the same typing scheme, it allows us and
> users to directly compare our results to the existing parameters.
> 2) pyrrolidine is a complicated molecule, and these complications are
> nicely described in Vanommeslaghe et al 2010, which is why we direct users
> to this paper and provide a link just above the screencasts.
>
> My advice for fexofenadine is to look through CGenFF and see what parts
> are already parameterized. Figure out what pieces you are missing, and
> design a scheme to fragment the structure into smaller pieces for
> parameterization. QM calculations on the full structure will be
> complicated and extremely computationally costly.
>
> Regards,
> Christopher Mayne
>
> On May 21, 2013, at 11:35 AM, Peterson J wrote:
>
> But how do you find these atom types? Does learning more about CGenFF
> and its atom typing scheme help a lot to understand the tutorials?
> What if I'm working on a completely new chemical compound for which no
> published values?
> I'm actually working fexofenadine and how would you advice me to find
> the atom types.
>
> Thanks,
> Peterson
>
>
> On Tue, May 21, 2013 at 7:59 AM, Mayne, Christopher G <
> cmayne2_at_illinois.edu> wrote:
>
>> I dropped NAMD-L from the cc list; as I said, this is a VMD issue.
>>
>> NG3C51 is the atom type, not the atom name. Since the tutorial shows a
>> full parameterization from scratch, the atom types can be anything. In
>> this case, for convenience I used the same atom typing scheme that is used
>> by CGenFF to allow for easy comparison to the published values.
>>
>> Regards,
>> Christopher Mayne
>>
>> On May 20, 2013, at 11:48 PM, Peterson J wrote:
>>
>> Hi,
>>
>> I just started following the screencast tutorials available for ffTK.
>> I'm not quite clear about renaming the added N atom from N1 to NG3C51 and
>> all other subsequent namings for C and H atoms. How are they named? Any
>> background information about the naming that is missing in the tutotrial?
>>
>> Thanks
>>
>>
>> On Mon, May 20, 2013 at 2:32 PM, Mayne, Christopher G <
>> cmayne2_at_illinois.edu> wrote:
>>
>>> Peterson,
>>>
>>> Since you're question is primarily regarding a VMD plugin, it is not
>>> particularly appropriate to cross post on NAMD-L.
>>>
>>> The web-based tools that you have mentioned differ in a very important
>>> way--they provide parameters based on analogy to molecules or molecular
>>> fragments that have already been parameterized and have been incorporated
>>> into the backend database. ffTK, in contrast, aides users in developing
>>> parameters directly from first principles and the workflow outlined for
>>> CGenFF. The primary advantage of the web-based services is their speed and
>>> ease of use. If you have a molecule that is highly analogous to something
>>> that has been worked out, then the results are generally pretty good. You
>>> should also note that ParamChem in particular indicates that users should
>>> assess the resulting parameters to determine if they are reasonable, and
>>> refine them if needed. In addition to a full parameterization from
>>> scratch, ffTK is suitable for conducting this refinement, and includes
>>> numerous metrics to assess parameter performance. The trade off, however,
>>> is that parameterization is a time consu!
>>> ming and frequently non-trivial process (we've tried to make it as
>>> streamlined as we can), and one should familiarize themselves with the
>>> principles underlying parameterization (e.g. CHARMM/CGenFF). The ffTK
>>> documentation website provides some information and links to relevant
>>> resources.
>>>
>>> Regards,
>>> Christopher Mayne
>>>
>>> On May 20, 2013, at 1:03 PM, Peterson J wrote:
>>>
>>> > Hi VMD and NAMD users,
>>> >
>>> > I'm very new to VMD and NAMD. I'm now in the process of parameterizing
>>> a ligand molecule. As I came across various a few web tools like paramchem,
>>> swissparam and so on. I have also seen VMD providing a plugin called
>>> Forcefield Toolkit calculating parameters using Gaussian and preparing the
>>> files for MD run using NAMD.
>>> >
>>> > I would like to get a few suggestion points on which one to use and
>>> the advantages and disadvantages over one another.
>>> >
>>> > What if I use one of the mentioned webtools instead of ffTk that use
>>> lengthy QM calculations to obtain the parameters?
>>> >
>>> > Thanks in advance for the suggestions.
>>> >
>>> > -Peterson
>>>
>>>
>>>
>>
>>
>
>