Re: [AMBER] loadPdbUsingSeq command

From: David A Case <>
Date: Tue, 14 Jun 2011 09:39:48 -0400

On Tue, Jun 14, 2011, David A Case wrote:

> > This is the tleap script that I have been using:
> >
> > source leaprc.ff03
> > loadamberparams parm99.dat
> > loadamberparams gaff.dat
> This is a very odd set of commands: you are loading the ff03 force field,
> but then over-riding the parameters with those from parm99.dat. This will
> yield some very strange mixture of ff03 and ff99 that you almost certainly
> don't want. I recommend you use either ff03 or ff10 (which is the same
> as ff99SB for a protein). The gaff.dat file is not used --shouldn't do
> any harm.

Let me clarify this a bit:

The leaprc.ff03 script does the following:

    parm99 = loadamberparams parm99.dat
    frcmod03 = loadamberparams frcmod.ff03

The upshot is that the parameters in the frcmod.ff03 file over-ride some
of the parameters in parm99.dat. If you then re-load parm99.dat, you get
back to the original (parm99) parameters, which, as I said, is almost
certainly not what you want.

...good luck...dac

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Received on Tue Jun 14 2011 - 07:00:03 PDT
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