Re: Re: vmd-l: Suggestions on parameterizing a ligand to simulate in NAMD

From: Peterson J (
Date: Mon May 20 2013 - 23:48:48 CDT


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?


On Mon, May 20, 2013 at 2:32 PM, Mayne, Christopher G

> 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

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