[gmx-users] amino acids in 43a1
spoel at xray.bmc.uu.se
Thu Aug 19 17:05:49 CEST 2004
On Thu, 2004-08-19 at 15:48, Arturas wrote:
> 1. Preparing my structures I have encauntered that aromatic amino acids
> in ff43a1 FF have "C" carbon type instead of "CR1" in aromatic rings.
> Are amino acids treated somehow different in GROMACS than other
> compounds ?
This is force field dependent.
> 2. gromos ff have "gromos type" column in *.rtp files with many
> different codes (e.g. ga_17, gi_1, etc.). What does it mean ??? I did
> not found any describtion in GROMACS manual.
These are in ffXXbon.itp
where XX is your force field.
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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