Re: [AMBER] parmchk doesn't recognize the changes made in leaprc.ff99SB and parm.99

From: Jason Swails <>
Date: Fri, 18 Oct 2013 09:55:07 -0400

On Fri, Oct 18, 2013 at 9:06 AM, Sajeewa Pemasinghe <>wrote:

> Hi all,
> I have a pyrophosphate residue in my protein pdb. According to J Comp Chem
> 2003, 24, 1016-1025 I need to create a new atom type O3. So in
> the /usr/local/amber11/dat/leap/cmd/leaprc.ff99SB I added the new atom type
> as
> { "O3" "O" "sp2" }

> and then in the /usr/local/amber11/dat/leap/parm/parm99.dat I made the
> necessary changes for mass, bond,angle,torsions.

I'll offer an unsolicited suggestion: Do not change these files. Once you
change leaprc.ff99SB or parm99.dat, you no longer have ff99SB or the ff99
parameters (which are subsequently used to define ff99SB). You can
implement any of these changes in your own leaprc file or an frcmod file.

> Now when I do
> parmchk -i pop.prep -f prepi -o pop.frcmod

> Still the pop.frcmod says
> O3 0.000 0.000 ATTN, need revision
> O3-P 0.00 0.000 ATTN, need revision
> O3-P -O3 0.000 0.000 ATTN, need revision
> O3-P -OS 0.000 0.000 ATTN, need revision
> O3-P -OS-P 1 0.000 0.000 0.000 ATTN, need
> revision
> Could any one please tell me why parmchk doesn't recognize the newly
> updated values for O3 atomtype or advise me if I have overlooked something?

By default, parmchk looks in gaff.dat. If you want parmchk to get the
parameters from parm99.dat, you need to use a command like

parmchk -i pop.prep -f prepi -o pop.frcmod -p

If you still get lines that say [ATTN, need revision], make the changes
directly in pop.frcmod rather than modifying the parm99.dat file (that's
why pop.frcmod is there). In fact, ff99SB is actually implemented by
loading parm99.dat and then using an frcmod file to redefine the 3 torsion
parameters that it fixed.

Also, parmchk doesn't do anything with leaprc files -- only leap uses those
files. The new atom type that you added does nothing except give leap a
little extra information about the O3 atom type you defined. I've never
found this to be necessary before, but in case what you are trying to do
requires this definition you can always add that command in your own leap


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Fri Oct 18 2013 - 07:00:15 PDT
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