On Fri, Dec 10, 2010 at 1:07 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> > RES = loadamberprep your_prep_file.prep
> > set RES head RES.1.ATOM
> > set RES tail RES.1.ATOM2
>
> It used to be that the RES name was defined in the prep file.
> If this is still the case, you would just need
>
> > loadamberprep your_prep_file.prep
>
> Not sure if setting 'RES =' could create a problem.
> Note that >1 residue type can be defined in a prep file.
>
This is true. Keep in mind the residue naming used in the prep files. (I
also think prep files can have a defined connect0/connect1 or head/tail) I'm
used to using mol2 files, in which case I make sure that the residue name in
the mol2 is the same as the residue name I assign it to, though I think in
the case of
RES = loadmol2 res.mol2
RES is the name of the residue... but I don't know for certain.
All the best,
Jason
> Bill
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Fri Dec 10 2010 - 11:30:04 PST
