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
Received on Mon May 09 2011 - 03:00:03 PDT
