Will AMBER 9 work instead of AMBER 12. I have only AMBER 9.
On Mon, Sep 16, 2013 at 9:59 AM, Jason Swails <jason.swails.gmail.com>wrote:
> On Mon, Sep 16, 2013 at 8:39 AM, sudipta <sudipta.mml.gmail.com> wrote:
>
> > On Mon, Sep 16, 2013 at 5:51 AM, Jason Swails <jason.swails.gmail.com
> > >wrote:
> >
> > > On Mon, Sep 16, 2013 at 12:45 AM, sudipta <sudipta.mml.gmail.com>
> wrote:
> > >
> > > > Hi Jason,
> > > >
> > > > I am facing another problem. The new .prmtop file which I generated
> > using
> > > > chamber is not compatable with NAMD. The NAMD program showing some
> > error
> > > > like
> > > > Processor 0 Exiting: Called CmiAbort ------------
> > > > Reason: FATAL ERROR: Failed to read AMBER parm file!
> > > >
> > > > Charm++ fatal error:
> > > > FATAL ERROR: Failed to read AMBER parm file!
> > >
> > >
> > > I am almost certain that NAMD does not (and probably never will) read
> > > chamber-generated topology files. Why do you need to run NAMD using a
> > > chamber-generated topology when you can just use the PSF file that you
> > gave
> > > to chamber directly?
> > >
> > > Yes, I can use the PSF file directly for running NAMD. But, I was
> trying
> > to see the compatibility of chamber generated .prmtop file with NAMD. I
> > never face any problem when I generate this file using tleap or xleap. I
> > think there are some formatting problem. It is hard to figure out where
> is
> > the problem for me because apparently both files looks like similar.
> >
> > > The _only_ thing you need to use chamber for is to run MM/PBSA
> > calculations
> > > using AmberTools after your NAMD simulations. Since your
> > chamber-generated
> > > topology file and your PSF file define equivalent Hamiltonians, you can
> > use
> > > either one and get the same results. The key is to use the one that
> will
> > > work for the program you're running.
> > >
> > > Of courese, I can use either for running namd. But, if chamber
> genereted
> > .prmtop file is not compatable with namd then I think that file also
> > incomapatable with MMPBSA.py for that reason. I did it previously for
> other
> > system but that time I genereted the .prmtop file using xleap. It is
> > difficult to understand for me where are the differences betweeen two
> > files. Any suggestions will be helpful in this regard.
> >
>
> This is not correct. The chamber-generated topology file is NOT compatible
> with NAMD. It has extra sections that NAMD does not recognize (for
> additional CHARMM terms like CMAP, Urey-Bradley, 'true' Improper torsions,
> etc.). When using Amber files, NAMD has been programmed *specifically* to
> recognize topology files created by tleap. Those generated by chamber are
> too different.
>
> The chamber-generated topology file is incompatible with NAMD, but it is
> compatible with MMPBSA.py. On the other hand, the PSF file is compatible
> with NAMD, but is incompatible with MMPBSA.py.
>
>
> > > However, when I generate a file using tleap then it is running. But
> > during
> > > >
> > > that time I need to use amber force filed which I don't want. Please
> give
> > > > some suggestions how do I use chamber generated .prmtop file for
> runnig
> > > > namd2 or mmpbsa.py program. Is there any tricks or do I need to
> change
> > > > format further? if so, how can I do that?
> > > >
> > >
> > > Use the PSF file with NAMD and use the chamber-generated prmtop with
> > Amber.
> > >
> > > Again, here I am trying to say there are formatting differences between
> > the two .prmtop files when they are generated by xleap or chamber.
>
>
> > Finally, I need only to run the MMPBSA.py program on NAMD generated .dcd
> > trajectory using CHARMM forece field field. Is there any other suitable
> > way to do that. I think if I can solve the compatibility prbolem between
> > the chamber and xleap generated files then my problem will solve. Please
> > help me in this regard.
> >
>
> The appropriate way to do this is as follows:
>
> 1) Generate your PSF file using whatever tool necessary
> 2) Run a simulation in NAMD with this PSF file.
> 3) Use chamber to generate a topology file compatible with cpptraj, sander,
> and pmemd from the PSF file you generated in step 1. (You also need to
> create the complex, receptor, and ligand topology files)
> 4) Run MMPBSA.py using the chamber-generated topology files you created in
> step 3 with the DCD file you created in step 2.
>
> An alternative is to use Amber for everything.
>
> 1) Generate your PSF file using whatever tool necessary
> 2) Use chamber to generate topology files
> 3) Run a simulation in pmemd or sander (part of Amber) using the topology
> files built in step 2.
> 4) Run MMPBSA.py using the chamber-generated topology files created in step
> 2 with the trajectory created in step 3.
>
> Note for both approaches, you need to have a copy of Amber 12 (AmberTools
> alone will not work). There is no other way to accomplish what you want to
> do using MMPBSA.py.
>
> Good luck,
> Jason
>
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Mon Sep 16 2013 - 08:30:03 PDT
