On May 24, 2012, at 8:21 AM, Jesper Sørensen <jesorensen.ucsd.edu> wrote:
> Hi Jason,
>
> Thanks for pointing me in the right direction. I have one follow up question. In the code snippet here below the C1, C2, and C3 atomtypes, am I correct if I think these are either united-atoms (e.g. CH3) or belonging to NA (e.g. C1')?
I'm not sure. Keep in mind this is atom type, not atom name. Therefore the nucleic acid reasoning is probably not justified (although still possible).
The atom types may be described via a comment in the parm*.dat files. You can also look at what atoms have these types in the standard library files (see
http://ambermd.org/formats.html for a description of the OFF library format do you can see which are the atom types).
The leap files are in AMBERHOME/dat/leap
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed May 23 2012 - 17:30:03 PDT
