Thank you very much Jason for all the advice. They gave me a lot of
insight. Actually modifying the parm99.dat was not necessary at the end
(whenever I do so I always keep a copy in case something goes wrong). I
just had to source the leaprc.ff99SB in tleap and then type addAtomTypes { {
"O3" "O" "sp2" } } for the new atom type mentioned in the frcmod and then
load my frcmod and prep files and then load the pdb
Thank you again
Sajeewa
On Fri, Oct 18, 2013 at 9:55 AM, Jason Swails <jason.swails.gmail.com>wrote:
> On Fri, Oct 18, 2013 at 9:06 AM, Sajeewa Pemasinghe <sajeewasp.gmail.com
> >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
> $AMBERHOME/dat/leap/parm/parm99.dat
>
> 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
> script.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Sat Oct 19 2013 - 13:00:03 PDT
