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
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri May 06 2011 - 18:00:02 PDT
