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

From: Jason Swails <>
Date: Mon, 16 Sep 2013 09:59:24 -0400

On Mon, Sep 16, 2013 at 8:39 AM, sudipta <> wrote:

> 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.

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 On the other hand, the PSF file is compatible
with NAMD, but is incompatible with

> > 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.

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 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 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

Good luck,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Mon Sep 16 2013 - 07:00:02 PDT
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