VMD-L Mailing List

From: Peterson J (peterson.jjjj_at_gmail.com)
Date: Thu Jun 13 2013 - 11:59:28 CDT

Continue talking about the analogical parameterization of the novel
molecules, is it a common procedure, if not at least meaningful, to combine
the parameters obtained from two different parameterizing tools for
instance Paramchem and Swissparam if they use different background
databases?
How similar are the parameters obtained from these tools?

-Peterson

On Tue, May 21, 2013 at 4:55 PM, Mayne, Christopher G
<cmayne2_at_illinois.edu>wrote:

> No, neither I nor ffTK will check ParamChem output for you. As a user,
> I can tell you that ParamChem reports a "penalty" indicating analogy to a
> molecule or molecular fragment with existing parameters (of implied
> quality). But I am not involved with developing ParamChem, so you should
> read the authors' papers for more information.
>
>
> On May 21, 2013, at 4:38 PM, Peterson J wrote:
>
> 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
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>
>>>
>>
>>
>
>