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

From: Jason Swails <>
Date: Mon, 23 Sep 2013 06:59:04 -0400

On Sun, Sep 22, 2013 at 7:13 PM, sudipta <> wrote:

> Hi Jason,
> I can run a NVT simulation using amber12 with chamber generated .prmtop
> file. However, I can't run the program. It shows some error
> like
> ValueError: invalid literal for int() with base 10: '8('
> Error occured on rank 2.
> Exiting. All files have been retained.

It would help if you could give me the full program output so I can see
where this error might be occurring. My guess is that it happens while
trying to read the topology files, but without the rest of the output it is
hard to tell.

If you are using PBS or some other scheduler, try to combine the error and
output streams. For Torque/PBS, you do that with

#PBS -j oe

or add "-j oe" to the qsub command-line.

In any case, if you could also send me the topology files that you use (the
ones generated by chamber) so I can try and debug, that would help. Please
send the topology files directly to me (not to the list).

> The command line is
> time mpirun -np 8 /home/sudipta/AMBER/amber12/bin/ -O -i
> 3jzb_complex_solv.prmtop -cp 3jzb_complex.prmtop -y
> 3jzb_protein_ligand_system_34.mdcrd > progress_mmpbsa.log
> [snip]
> and the namd generated .dcd file was converted to .mdcrd file by using the
> following command line

I believe I've said this before, but converting the trajectory is NOT
necessary. will handle any type of trajectory that cpptraj does
(that includes NetCDF Amber, ASCII Amber, CHARMM/NAMD dcd, Gromacs
trajectories, etc.). So for the sake of debugging, please use the
original DCD file so we can rule out the conversion process as a source of
any possible mistakes (although I see no mistakes in the simple cpptraj
script shown below).

All the best,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Mon Sep 23 2013 - 04:00:03 PDT
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