From: Peterson J (
Date: Tue May 21 2013 - 11:35:01 CDT

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.


On Tue, May 21, 2013 at 7:59 AM, Mayne, Christopher G

> 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 <
>> 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