From: Jason Swails (jason.swails_at_gmail.com)
Date: Mon Sep 16 2013 - 04:55:09 CDT
Since this question was asked on the Amber mailing list, I'll post my
answer from there:
On Mon, Sep 16, 2013 at 12:51 AM, sudipta <sudipta.mml_at_gmail.com> wrote:
> Hi All,
>
> I am facing a problem to run a simulation where the .prmtop file was
> generated by CHAMBER (AMBERTOOLS 13). 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?
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.
> 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 program. Although, I can use directly CHARMM force field for running
> namd2. But I don't want that because, I want to use ambertools after
> getting the trajectories. 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.
Good luck,
Jason
-- Jason M. Swails BioMaPS, Rutgers University Postdoctoral Researcher
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