VMD-L Mailing List

From: Peterson J (peterson.jjjj_at_gmail.com)
Date: Tue May 21 2013 - 16:38:07 CDT

Thanks, but do you check if the parameters obtained are reasonable or not?

Peterson

On Tue, May 21, 2013 at 3:46 PM, Mayne, Christopher G
<cmayne2_at_illinois.edu>wrote:

> Peterson,
>
> You might also check out ParamChem for fexofenadine. It could be a good
> place to get reasonable starting parameters that could be refined using
> ffTK.
>
> Christopher
>
>
>
> On May 21, 2013, at 2:24 PM, Peterson J wrote:
>
> 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
>>>>
>>>>
>>>>
>>>
>>>
>>
>>
>
>