AMBER Archive (2006)

Subject: Re: AMBER: problem in saving parameter file for non-standard residue

From: David A. Case (case_at_scripps.edu)
Date: Mon Jan 16 2006 - 13:44:22 CST

On Mon, Jan 16, 2006, Ross Walker wrote:
>
> No, you do not, the leaprc files are scripts that load both the templates
> for specific residues and the parameter files. However, if say you wanted to
> use the FF94 force field for you protein but the GAFF force field for your
> ligand then you would do:
>
> source leaprc.ff94
> loadamberparams gaff.dat
>
> sourcing both the leaprc.ff94 script and the leaprc.gaff script could cause
> problems and so it is best to avoid this. I hope this makes sense.

Ross is usually correct, but I don't agree with him here: you *should* source
both leaprc.ff94 and leaprc.gaff if you want both force fields. This will
give you the hybridizations and elements for the gaff atoms types. (Ross:
take a look at what leaprc.gaff does....)

....dac

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