VMD-L Mailing List

From: Peterson J (peterson.jjjj_at_gmail.com)
Date: Thu Jun 13 2013 - 17:08:29 CDT

Your explanation gives me a good understanding on the parameters obtained
from these sources. Thanks for the references too.

-Peterson

On Thu, Jun 13, 2013 at 3:55 PM, Mayne, Christopher G
<cmayne2_at_illinois.edu>wrote:

> I'm not familiar with the differences in methodology for identifying
> analogous structures. You might see:
>
> J. Chem. Inf. Model. 2012, 52, 3144–3154
> J. Chem. Inf. Model. 2012, 52, 3155–3168
> J. Comp. Chem. 2011, 32, 2359–2368
>
> It is clear, however, that ParamChem and SwissParam assign existing
> parameters from different sources. ParamChem assigns parameters from a
> database of molecules that have already been parameterized for CHARMM and
> CHARMM-compatible (i.e., CGenFF) parameters. SwissParam, however, provides
> vdW terms from analogous CHARMM atom types, but takes bonded terms (bonds,
> angles, dihedrals) from MMFF. It is my opinion that it is generally a poor
> idea to combine parameters from different force fields, particularly in the
> case of an empirical FFs with different parameterization philosophy, as
> they tend to be highly tuned for self consistency. Without running
> calculations for specific test cases, it is difficult to make a general
> statement about comparing and/or combining the output from these two
> resources.
>
> Christopher Mayne
>
>
> On Jun 13, 2013, at 11:59 AM, Peterson J wrote:
>
> 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
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>
>>>
>>
>>
>
>