Hello,
That's because sleap has a bug in which it doesn't allow you to change the
mbondi radii set. I'm working on a script that will let you change the
radius set of any prmtop which I'll release shortly (it's the only way you
can get the mbondi3 radius set for igb = 8), but it's been on the back
burner for a little bit.
If you want, you can use --ignore-warnings to force it to create a cpin
file, but you'll have to re-run the reference compounds to make sure that
the titration curves come out normally.
Or perhaps we can get together a patch for sleap to fix the issue of setting
the correct bondi set.
All the best,
Jason
On Mon, May 9, 2011 at 11:55 AM, pankhuri arora <pankhuri2001.gmail.com>wrote:
> Hi Jason,
>
> Thanks for the suggestion. I tried to create the cpin file with the
> following command:
>
> /amber11/AmberTools/bin/cpinutil -p prmtop -igb 2 -notresname TYR, LYS >
> cpin
>
> but again got the same error;
>
> Error: mbondi2 radius set should be used for constant pH simulations. All
> reference energies were calculated using these radii! Set --ignore-warnings
> to ignore this warning.
>
> Regards,
> Pankhuri
>
> On Sat, May 7, 2011 at 5:33 AM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
> > Hi Pankhuri,
> >
> > My comments are below:
> >
> > On Thu, May 5, 2011 at 7:34 AM, pankhuri arora <pankhuri2001.gmail.com
> > >wrote:
> >
> > > Dear Amber Users,
> > >
> > > I am trying to do a constant pH simulation on a protein-ligand complex
> > with
> > > Amber11 , where the ligand is a sugar ( GlcNAc )6 . I generated the
> > > topology
> > > file with the following command
> > >
> > > sleap -f leap.in
> > >
> > > and the commands in the leap.in file are:
> > >
> > > source leaprc.GLYCAM_06
> > > source leaprc.constph
> > > set default PBRadii mbondi2
> > > complex = loadpdb HEL_GlcNAc6_HC2_301-500ps_ave.pdb
> > > saveAmberParm complex prmtop prmcrd
> > > quit
> > >
> > > and I got the following output :
> > >
> > > Warning: there is an atom HE2 in residue GL442 which does not exist in
> > the
> > > model GL4! This atom will not be created.
> > >
> > > Then I did energy minimization with the following parameters:
> > > Run minimization
> > > # 5000 steps of minimization, generalized Born solvent model
> > > &cntrl
> > > imin=1, ntmin=1, maxcyc=5000, ncyc=2500,
> > > cut=30.0, igb=2, saltcon=0.1
> > > ntx=1, irest=0, ntb=0, ntpr=5
> > > ntc=1, ntf=1,
> > > ntwx=10, ntwv=10, ntwe=10, ntwr=10
> > > /
> > >
> > > After minimizing the system, I tried to create a cpin file with the
> > > following command :
> > >
> > > /amber11/AmberTools/bin/ambpdb -p prmtop < restrt |
> > > /amber11/AmberTools/bin/cpinutil -notresname TYR,LYS > cpin
> > >
> >
> > This is not the correct way to use cpinutil (which is a python script
> now).
> > Now, use it as the following:
> >
> > cpinutil -p <prmtop> -igb 2 -notresname TYR, LYS > cpin
> >
> >
> > >
> > > and got the following error:
> > >
> > > | New format PARM file being parsed.
> > > | Version = 1.000 Date = 05/22/06 Time = 12:10:21
> > > Warning: igb value not specified. igb = 5 used as default. Be sure to
> use
> > > this value for your constant pH simulations!
> > > Error: mbondi2 radius set should be used for constant pH simulations.
> All
> > > reference energies were calculated using these radii! Set
> > --ignore-warnings
> > > to ignore this warning.
> > >
> >
> > See if you still get this warning. If you do, I think it's because sleap
> > doesn't actually set the pbradii set properly. If this is the case, I
> can
> > attach a script that will alter the radii sets for you to match what it
> > should be. You NEED the mbondi2 radii (since that's how the reference
> > compounds were parametrized), but I don't think sleap prints them out
> > correctly yet.
> >
> > HTH,
> > Jason
> >
> >
> > > I dont know why this error is coming because I have already set default
> > > PBRadii mbondi2 in the leap.in file and the ibg value to 2 during the
> > > energy
> > > minimization. I tried the minimization with igb=5 but again got the
> same
> > > error while creating the cpin file
> > >
> > > Any suggestions please? Thanks in advance
> > >
> > > Regards,
> > > Pankhuri
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon May 09 2011 - 08:00:06 PDT
