Re: [AMBER] phosphorylated residues

From: Jason Swails <>
Date: Fri, 10 Dec 2010 14:01:50 -0500

On Fri, Dec 10, 2010 at 1:07 PM, Bill Ross <> 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,

> Bill
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Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Fri Dec 10 2010 - 11:30:04 PST
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