Re: vmd-l: FFTK Atom types

From: Mayne, Christopher G (
Date: Wed Mar 27 2013 - 08:06:05 CDT

You're best bet is to look through the CHARMM topology files, specifically at the MASS statements, or through the parameter files, specifically at the NONBONDED section. You can also load the CHARMM27 topology and parameter files into the parameter browser within the BuildPar tab of ffTK, where it will parse out relevant comments for each atom type and allow you to filter by element (e.g., isolate all nitrogen atom types). It's also worth digging through the various stream files that are included in the CHARMM distributions, as that is where less commonly used chemical functionalities tend to appear. A third place to look is a search of the CHARMM user forums, where you might find a thread related to NO parameters.

Christopher Mayne

On Mar 27, 2013, at 2:21 AM, Francesco Pietra wrote:

> Hello:
> I am looking for a comprehensive list of atom types for charmm27 ff to
> use with namd/vmd/fftk. I was only able to find partial lists, such as
> at <>
> With inorganic molecules, such as NO, the selection of atom types is
> not obvious (for me). With NO I placed in FFTK atom type NO2 for
> nitrogen and atom type OM for oxygen (tentatively). H-F optimization
> was carried out but I am still in doubt.
> Thanks
> francesco pietra

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