Re: [AMBER] How do I use for namd .dcd file?

From: sudipta <>
Date: Mon, 16 Sep 2013 08:39:25 -0400

On Mon, Sep 16, 2013 at 5:51 AM, Jason Swails <>wrote:

> On Mon, Sep 16, 2013 at 12:45 AM, sudipta <> 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 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.

> 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 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 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.

> Good luck,
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Mon Sep 16 2013 - 06:00:05 PDT
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